diff --git a/auto_rx/auto_rx.py b/auto_rx/auto_rx.py
index b5f18729..83610a4b 100644
--- a/auto_rx/auto_rx.py
+++ b/auto_rx/auto_rx.py
@@ -8,6 +8,16 @@
 #   Refer github page for instructions on setup and usage.
 #   https://github.com/projecthorus/radiosonde_auto_rx/
 #
+
+# exit status codes:
+#
+# 0 - normal termination (ctrl-c)
+# 1 - critical error, needs human attention to fix
+# 2 - exit because continous running timeout reached
+# 3 - exception occurred, can rerun after resetting SDR
+# 4 - some of the threads failed to join, SDR reset and restart required
+#     this is mostly caused by hung external utilities
+
 import argparse
 import datetime
 import logging
@@ -44,6 +54,7 @@
     start_flask,
     stop_flask,
     flask_emit_event,
+    flask_running,
     WebHandler,
     WebExporter,
 )
@@ -322,7 +333,7 @@ def handle_scan_results():
                     if (type(_key) == int) or (type(_key) == float):
                         # Extract the currently decoded sonde type from the currently running decoder.
                         _decoding_sonde_type = autorx.task_list[_key]["task"].sonde_type
-                        
+
                         # Remove any inverted decoder information for the comparison.
                         if _decoding_sonde_type.startswith("-"):
                             _decoding_sonde_type = _decoding_sonde_type[1:]
@@ -806,6 +817,11 @@ def main():
     logging.getLogger("engineio").setLevel(logging.ERROR)
     logging.getLogger("geventwebsocket").setLevel(logging.ERROR)
 
+    # Check all the RS utilities exist.
+    logging.debug("Checking if utils exist")
+    if not check_rs_utils():
+        sys.exit(1)
+
     # Attempt to read in config file
     logging.info("Reading configuration file...")
     _temp_cfg = read_auto_rx_config(args.config)
@@ -844,9 +860,6 @@ def main():
     web_handler = WebHandler()
     logging.getLogger().addHandler(web_handler)
 
-    # Check all the RS utilities exist.
-    if not check_rs_utils():
-        sys.exit(1)
 
     # If a sonde type has been provided, insert an entry into the scan results,
     # and immediately start a decoder. This also sets the decoder time to 0, which
@@ -1074,7 +1087,7 @@ def main():
             logging.info("Shutdown time reached. Closing.")
             stop_flask(host=config["web_host"], port=config["web_port"])
             stop_all()
-            break
+            sys.exit(2)
 
 
 if __name__ == "__main__":
@@ -1085,9 +1098,13 @@ def main():
         # Upon CTRL+C, shutdown all threads and exit.
         stop_flask(host=config["web_host"], port=config["web_port"])
         stop_all()
+        sys.exit(0)
     except Exception as e:
         # Upon exceptions, attempt to shutdown threads and exit.
         traceback.print_exc()
         print("Main Loop Error - %s" % str(e))
-        stop_flask(host=config["web_host"], port=config["web_port"])
+        if flask_running():
+            stop_flask(host=config["web_host"], port=config["web_port"])
         stop_all()
+        sys.exit(3)
+
diff --git a/auto_rx/auto_rx.sh b/auto_rx/auto_rx.sh
index a8a1b567..6c901cd3 100755
--- a/auto_rx/auto_rx.sh
+++ b/auto_rx/auto_rx.sh
@@ -6,7 +6,9 @@
 # NOTE: If running this from crontab, make sure to set the appropriate PATH env-vars,
 # else utilities like rtl_power and rtl_fm won't be found.
 #
-#	WARNING - THIS IS DEPRECATED - PLEASE USE THE SYSTEMD SERVICE
+#	WARNING - THIS IS DEPRECATED - PLEASE USE THE SYSTEMD SERVICE OR DOCKER IMAGE
+#   See: https://github.com/projecthorus/radiosonde_auto_rx/wiki#451-option-1---operation-as-a-systemd-service-recommended
+#   Or: https://github.com/projecthorus/radiosonde_auto_rx/wiki/Docker
 #
 
 # change into appropriate directory
@@ -15,7 +17,4 @@ cd $(dirname $0)
 # Clean up old files
 rm log_power*.csv
 
-# Start auto_rx process with a 3 hour timeout.
-# auto_rx will exit after this time.
-
-python3 auto_rx.py -t 180
+python3 auto_rx.py -t 180
\ No newline at end of file
diff --git a/auto_rx/autorx/__init__.py b/auto_rx/autorx/__init__.py
index a108510c..df2b5a84 100644
--- a/auto_rx/autorx/__init__.py
+++ b/auto_rx/autorx/__init__.py
@@ -12,7 +12,7 @@
 # MINOR - New sonde type support, other fairly big changes that may result in telemetry or config file incompatability issus.
 # PATCH - Small changes, or minor feature additions.
 
-__version__ = "1.6.2-beta4"
+__version__ = "1.6.2-beta5"
 
 
 # Global Variables
diff --git a/auto_rx/autorx/aprs.py b/auto_rx/autorx/aprs.py
index eb864496..747eeaa0 100644
--- a/auto_rx/autorx/aprs.py
+++ b/auto_rx/autorx/aprs.py
@@ -759,13 +759,19 @@ def close(self):
 
         # Wait for all threads to close.
         if self.upload_thread is not None:
-            self.upload_thread.join()
+            self.upload_thread.join(60)
+            if self.upload_thread.is_alive():
+                self.log_error("aprs upload thread failed to join")
 
         if self.timer_thread is not None:
-            self.timer_thread.join()
+            self.timer_thread.join(60)
+            if self.timer_thread.is_alive():
+                self.log_error("aprs timer thread failed to join")
 
         if self.input_thread is not None:
-            self.input_thread.join()
+            self.input_thread.join(60)
+            if self.input_thread.is_alive():
+                self.log_error("aprs input thread failed to join")
 
     def log_debug(self, line):
         """ Helper function to log a debug message with a descriptive heading. 
diff --git a/auto_rx/autorx/config.py b/auto_rx/autorx/config.py
index f9b9a56d..ff04798b 100644
--- a/auto_rx/autorx/config.py
+++ b/auto_rx/autorx/config.py
@@ -883,7 +883,7 @@ def read_auto_rx_config(filename, no_sdr_test=False):
         if len(auto_rx_config["sdr_settings"].keys()) == 0:
             # We have no SDRs to use!!
             logging.error("Config - No working SDRs! Cannot run...")
-            return None
+            raise SystemError("No working SDRs!")
         else:
             # Create a global copy of the configuration file at this point
             global_config = copy.deepcopy(auto_rx_config)
@@ -902,7 +902,8 @@ def read_auto_rx_config(filename, no_sdr_test=False):
             web_password = auto_rx_config["web_password"]
 
             return auto_rx_config
-
+    except SystemError as e:
+        raise e
     except:
         traceback.print_exc()
         logging.error("Could not parse config file.")
diff --git a/auto_rx/autorx/email_notification.py b/auto_rx/autorx/email_notification.py
index 4a8f972c..6e66b4bf 100644
--- a/auto_rx/autorx/email_notification.py
+++ b/auto_rx/autorx/email_notification.py
@@ -379,7 +379,9 @@ def close(self):
         self.input_processing_running = False
 
         if self.input_thread is not None:
-            self.input_thread.join()
+            self.input_thread.join(60)
+            if self.input_thread.is_alive():
+                self.log_error("email notification input thread failed to join")
 
     def running(self):
         """ Check if the logging thread is running.
diff --git a/auto_rx/autorx/gpsd.py b/auto_rx/autorx/gpsd.py
index bdd8d8e1..ac19782a 100644
--- a/auto_rx/autorx/gpsd.py
+++ b/auto_rx/autorx/gpsd.py
@@ -335,7 +335,9 @@ def close(self):
         self.gpsd_thread_running = False
         # Wait for the thread to close.
         if self.gpsd_thread != None:
-            self.gpsd_thread.join()
+            self.gpsd_thread.join(60)
+            if self.gpsd_thread.is_alive():
+                logging.error("GPS thread failed to join")
 
     def send_to_callback(self, data):
         """
diff --git a/auto_rx/autorx/habitat.py b/auto_rx/autorx/habitat.py
index ebb4303b..f76c4299 100644
--- a/auto_rx/autorx/habitat.py
+++ b/auto_rx/autorx/habitat.py
@@ -831,13 +831,20 @@ def close(self):
 
         # Wait for all threads to close.
         if self.upload_thread is not None:
-            self.upload_thread.join()
+            self.upload_thread.join(60)
+            if self.upload_thread.is_alive():
+                self.log_error("habitat upload thread failed to join")
+
 
         if self.timer_thread is not None:
-            self.timer_thread.join()
+            self.timer_thread.join(60)
+            if self.timer_thread.is_alive():
+                self.log_error("habitat timer thread failed to join")
 
         if self.input_thread is not None:
-            self.input_thread.join()
+            self.input_thread.join(60)
+            if self.input_thread.is_alive():
+                self.log_error("habitat input thread failed to join")
 
     def log_debug(self, line):
         """ Helper function to log a debug message with a descriptive heading. 
diff --git a/auto_rx/autorx/log_files.py b/auto_rx/autorx/log_files.py
index 6a595bfc..95eefde0 100644
--- a/auto_rx/autorx/log_files.py
+++ b/auto_rx/autorx/log_files.py
@@ -455,9 +455,8 @@ def calculate_skewt_data(
                 break
 
         except Exception as e:
-            print(str(e))
-
-        # Continue through the data..
+            logging.exception(f"Exception {str(e)} in calculate_skewt_data")
+            raise
 
     return _skewt
 
diff --git a/auto_rx/autorx/ozimux.py b/auto_rx/autorx/ozimux.py
index a3c8ce84..685a6910 100644
--- a/auto_rx/autorx/ozimux.py
+++ b/auto_rx/autorx/ozimux.py
@@ -252,7 +252,9 @@ def close(self):
         self.input_processing_running = False
 
         if self.input_thread is not None:
-            self.input_thread.join()
+            self.input_thread.join(60)
+            if self.input_thread.is_alive():
+                self.log_error("ozimux input thread failed to join")
 
     def log_debug(self, line):
         """ Helper function to log a debug message with a descriptive heading. 
diff --git a/auto_rx/autorx/rotator.py b/auto_rx/autorx/rotator.py
index 5301cf80..82ee374c 100644
--- a/auto_rx/autorx/rotator.py
+++ b/auto_rx/autorx/rotator.py
@@ -320,7 +320,9 @@ def close(self):
         self.rotator_thread_running = False
 
         if self.rotator_thread is not None:
-            self.rotator_thread.join()
+            self.rotator_thread.join(60)
+            if self.rotator_thread.is_alive():
+                self.log_error("rotator control thread failed to join")
 
         self.log_debug("Stopped rotator control thread.")
 
diff --git a/auto_rx/autorx/scan.py b/auto_rx/autorx/scan.py
index 1077c5ee..fe71746a 100644
--- a/auto_rx/autorx/scan.py
+++ b/auto_rx/autorx/scan.py
@@ -9,6 +9,7 @@
 import logging
 import numpy as np
 import os
+import sys
 import platform
 import subprocess
 import time
@@ -22,6 +23,7 @@
     reset_rtlsdr_by_serial,
     reset_all_rtlsdrs,
     peak_decimation,
+    timeout_cmd
 )
 from .sdr_wrappers import test_sdr, reset_sdr, get_sdr_name, get_sdr_iq_cmd, get_sdr_fm_cmd, get_power_spectrum
 
@@ -91,18 +93,10 @@ def run_rtl_power(
     if os.path.exists(filename):
         os.remove(filename)
 
-    # Add -k 30 option, to SIGKILL rtl_power 30 seconds after the regular timeout expires.
-    # Note that this only works with the GNU Coreutils version of Timeout, not the IBM version,
-    # which is provided with OSX (Darwin).
-    if "Darwin" in platform.platform():
-        timeout_kill = ""
-    else:
-        timeout_kill = "-k 30 "
-
     rtl_power_cmd = (
-        "timeout %s%d %s %s-f %d:%d:%d -i %d -1 -c 25%% -p %d -d %s %s%s"
+        "%s %d %s %s-f %d:%d:%d -i %d -1 -c 25%% -p %d -d %s %s%s"
         % (
-            timeout_kill,
+            timeout_cmd(),
             dwell + 10,
             rtl_power_path,
             bias_option,
@@ -314,7 +308,7 @@ def detect_sonde(
 
     if _mode == "IQ":
         # IQ decoding
-        rx_test_command = f"timeout {dwell_time * 2} "
+        rx_test_command = f"{timeout_cmd()} {dwell_time * 2} "
 
         rx_test_command += get_sdr_iq_cmd(
             sdr_type=sdr_type,
@@ -331,8 +325,9 @@ def detect_sonde(
         )
 
         # rx_test_command = (
-        #     "timeout %ds %s %s-p %d -d %s %s-M raw -F9 -s %d -f %d 2>/dev/null |"
+        #     "%s %ds %s %s-p %d -d %s %s-M raw -F9 -s %d -f %d 2>/dev/null |"
         #     % (
+        #         timeout_cmd(),
         #         dwell_time * 2,
         #         rtl_fm_path,
         #         bias_option,
@@ -360,7 +355,7 @@ def detect_sonde(
 
         # Sample Source (rtl_fm)
 
-        rx_test_command = f"timeout {dwell_time * 2} "
+        rx_test_command = f"{timeout_cmd()} {dwell_time * 2} "
 
         rx_test_command += get_sdr_fm_cmd(
             sdr_type=sdr_type,
@@ -379,8 +374,9 @@ def detect_sonde(
         )
 
         # rx_test_command = (
-        #     "timeout %ds %s %s-p %d -d %s %s-M fm -F9 -s %d -f %d 2>/dev/null |"
+        #     "%s %ds %s %s-p %d -d %s %s-M fm -F9 -s %d -f %d 2>/dev/null |"
         #     % (
+        #         timeout_cmd(),
         #         dwell_time * 2,
         #         rtl_fm_path,
         #         bias_option,
@@ -783,9 +779,9 @@ def __init__(
     def start(self):
         # Start the scan loop (if not already running)
         if self.sonde_scan_thread is None:
-            self.sonde_scanner_running = True
             self.sonde_scan_thread = Thread(target=self.scan_loop)
             self.sonde_scan_thread.start()
+            self.sonde_scanner_running = True
         else:
             self.log_warning("Sonde scan already running!")
 
@@ -854,26 +850,32 @@ def scan_loop(self):
                     sdr_hostname = self.sdr_hostname, 
                     sdr_port = self.sdr_port
                 )
-
-                time.sleep(10)
+                for _ in range(10):
+                    if not self.sonde_scanner_running:
+                        break
+                    time.sleep(1)
                 continue
             except Exception as e:
                 traceback.print_exc()
                 self.log_error("Caught other error: %s" % str(e))
-                time.sleep(10)
+                for _ in range(10):
+                    if not self.sonde_scanner_running:
+                        break
+                    time.sleep(1)
             else:
                 # Scan completed successfuly! Reset the error counter.
                 self.error_retries = 0
 
             # Sleep before starting the next scan.
-            for i in range(self.scan_delay):
-                time.sleep(1)
-                if self.sonde_scanner_running == False:
+            for _ in range(self.scan_delay):
+                if not self.sonde_scanner_running:
                     self.log_debug("Breaking out of scan loop.")
                     break
+                time.sleep(1)
 
         self.log_info("Scanner Thread Closed.")
         self.sonde_scanner_running = False
+        self.sonde_scanner_thread = None
 
     def sonde_search(self, first_only=False):
         """Perform a frequency scan across a defined frequency range, and test each detected peak for the presence of a radiosonde.
@@ -1143,12 +1145,16 @@ def oneshot(self, first_only=False):
 
     def stop(self, nowait=False):
         """Stop the Scan Loop"""
-        self.log_info("Waiting for current scan to finish...")
-        self.sonde_scanner_running = False
+        if self.sonde_scanner_running:
+            self.log_info("Waiting for current scan to finish...")
+            self.sonde_scanner_running = False
 
-        # Wait for the sonde scanner thread to close, if there is one.
-        if self.sonde_scan_thread != None and (not nowait):
-            self.sonde_scan_thread.join()
+            # Wait for the sonde scanner thread to close, if there is one.
+            if self.sonde_scan_thread != None and (not nowait):
+                self.sonde_scan_thread.join(60)
+                if self.sonde_scan_thread.is_alive():
+                    self.log_error("Scanning thread did not finish, terminating")
+                    sys.exit(4)
 
     def running(self):
         """Check if the scanner is running"""
diff --git a/auto_rx/autorx/sdr_wrappers.py b/auto_rx/autorx/sdr_wrappers.py
index 62af89d1..2b187ad2 100644
--- a/auto_rx/autorx/sdr_wrappers.py
+++ b/auto_rx/autorx/sdr_wrappers.py
@@ -11,7 +11,7 @@
 import subprocess
 import numpy as np
 
-from .utils import rtlsdr_test, reset_rtlsdr_by_serial, reset_all_rtlsdrs
+from .utils import rtlsdr_test, reset_rtlsdr_by_serial, reset_all_rtlsdrs, timeout_cmd
 
 
 def test_sdr(
@@ -67,7 +67,7 @@ def test_sdr(
             return False
 
         _cmd = (
-            f"timeout 10 "  # Add a timeout, because connections to non-existing IPs seem to block.
+            f"{timeout_cmd()} 10 "  # Add a timeout, because connections to non-existing IPs seem to block.
             f"{ss_iq_path} "
             f"-f {check_freq} "
             f"-s 48000 "
@@ -480,17 +480,7 @@ def get_power_spectrum(
         if os.path.exists(_log_filename):
             os.remove(_log_filename)
 
-
-        # Add -k 30 option, to SIGKILL rtl_power 30 seconds after the regular timeout expires.
-        # Note that this only works with the GNU Coreutils version of Timeout, not the IBM version,
-        # which is provided with OSX (Darwin).
-        _platform = platform.system()
-        if "Darwin" in _platform:
-            _timeout_kill = ""
-        else:
-            _timeout_kill = "-k 30 "
-
-        _timeout_cmd = f"timeout {_timeout_kill}{integration_time+10}"
+        _timeout_cmd = f"{timeout_cmd()} {integration_time+10} "
 
         _gain = ""
         if gain:
@@ -564,17 +554,7 @@ def get_power_spectrum(
         if os.path.exists(_log_filename):
             os.remove(_log_filename)
 
-
-        # Add -k 30 option, to SIGKILL rtl_power 30 seconds after the regular timeout expires.
-        # Note that this only works with the GNU Coreutils version of Timeout, not the IBM version,
-        # which is provided with OSX (Darwin).
-        _platform = platform.system()
-        if "Darwin" in _platform:
-            _timeout_kill = ""
-        else:
-            _timeout_kill = "-k 30 "
-
-        _timeout_cmd = f"timeout {_timeout_kill}{integration_time+10}"
+        _timeout_cmd = f"{timeout_cmd()} {integration_time+10} "
 
         _frequency_centre = int(frequency_start + (frequency_stop-frequency_start)/2.0)
 
diff --git a/auto_rx/autorx/utils.py b/auto_rx/autorx/utils.py
index 8e502faa..9a016afc 100644
--- a/auto_rx/autorx/utils.py
+++ b/auto_rx/autorx/utils.py
@@ -19,6 +19,7 @@
 import time
 import numpy as np
 import semver
+import shutil
 from dateutil.parser import parse
 from datetime import datetime, timedelta
 from math import radians, degrees, sin, cos, atan2, sqrt, pi
@@ -45,6 +46,21 @@
     "iq_dec"
 ]
 
+_timeout_cmd = None
+
+def timeout_cmd():
+    global _timeout_cmd
+    if not _timeout_cmd:
+        t=shutil.which("gtimeout")
+        if t:
+            _timeout_cmd = "gtimeout -k 30 "
+        else:
+            if not shutil.which("timeout"):
+                logging.critical("timeout command-line tool not present in system. try installing gtimeout.")
+                sys.exit(1)
+            else:
+                _timeout_cmd = "timeout -k 30 "
+    return _timeout_cmd
 
 def check_rs_utils():
     """ Check the required RS decoder binaries exist
@@ -54,7 +70,7 @@ def check_rs_utils():
         if not os.path.isfile(_file):
             logging.critical("Binary %s does not exist - did you run build.sh?" % _file)
             return False
-
+        _ = timeout_cmd()
     return True
 
 
@@ -776,10 +792,10 @@ def is_rtlsdr(vid, pid):
 def reset_rtlsdr_by_serial(serial):
     """ Attempt to reset a RTLSDR with a provided serial number """
 
-    # If not Linux, return immediately.
+    # If not Linux, raise exception and let auto_rx.py convert it to exit status code.
     if is_not_linux():
         logging.debug("RTLSDR - Not a native Linux system, skipping reset attempt.")
-        return
+        raise SystemError("SDR unresponsive")
 
     lsusb_info = lsusb()
     bus_num = None
@@ -853,10 +869,10 @@ def find_rtlsdr(serial=None):
 def reset_all_rtlsdrs():
     """ Reset all RTLSDR devices found in the lsusb tree """
 
-    # If not Linux, return immediately.
+    # If not Linux, raise exception and let auto_rx.py convert it to exit status code.
     if is_not_linux():
         logging.debug("RTLSDR - Not a native Linux system, skipping reset attempt.")
-        return
+        raise SystemError("SDR unresponsive")
 
     lsusb_info = lsusb()
     bus_num = None
@@ -906,11 +922,12 @@ def rtlsdr_test(device_idx="0", rtl_sdr_path="rtl_sdr", retries=5):
         logging.debug("RTLSDR - TCP Device, skipping RTLSDR test step.")
         return True
 
-    _rtl_cmd = "timeout 5 %s -d %s -n 200000 - > /dev/null" % (
+    _rtl_cmd = "%s 5 %s -d %s -f 400000000 -n 200000 - > /dev/null" % (
+        timeout_cmd(),
         rtl_sdr_path,
         str(device_idx),
     )
-
+    
     # First, check if the RTLSDR with a provided serial number is present.
     if device_idx == "0":
         # Check for the presence of any RTLSDRs.
diff --git a/auto_rx/autorx/web.py b/auto_rx/autorx/web.py
index 4457d4e7..9911ec34 100644
--- a/auto_rx/autorx/web.py
+++ b/auto_rx/autorx/web.py
@@ -49,7 +49,7 @@
 # This thread will hold the currently running flask application thread.
 flask_app_thread = None
 # A key that needs to be matched to allow shutdown.
-flask_shutdown_key = "temp"
+flask_shutdown_key = None
 
 # SocketIO instance
 socketio = SocketIO(app, async_mode="threading")
@@ -289,6 +289,9 @@ def flask_get_log_list():
     """ Return a list of log files, as a list of objects """
     return json.dumps(list_log_files(quicklook=True))
 
+def flask_running():
+    global flask_shutdown_key
+    return flask_shutdown_key is not None
 
 @app.route("/get_log_by_serial/<serial>")
 def flask_get_log_by_serial(serial):