diff --git a/src/main/scala/com/typesafe/sbt/packager/GenericPackageSettings.scala b/src/main/scala/com/typesafe/sbt/packager/GenericPackageSettings.scala
index f9e7d0e9c..80a8b5868 100644
--- a/src/main/scala/com/typesafe/sbt/packager/GenericPackageSettings.scala
+++ b/src/main/scala/com/typesafe/sbt/packager/GenericPackageSettings.scala
@@ -88,7 +88,7 @@ trait GenericPackageSettings
           if !file.isDirectory
           if name startsWith "bin/"
           if !(name endsWith ".bat")  // IGNORE windows-y things.
-        } yield LinuxSymlink("/usr/" + name, installLocation+"/"+pkg+"/"+name)
+        } yield LinuxSymlink("/usr/" + name, installLocation.stripPrefix("/usr/")+"/"+pkg+"/"+name)
     },
     // Map configuration files
     linuxPackageSymlinks <++= (normalizedName in Universal, mappings in Universal, defaultLinuxInstallLocation) map { (pkg, mappings, installLocation) =>
diff --git a/src/main/scala/com/typesafe/sbt/packager/archetypes/JavaServerApplication.scala b/src/main/scala/com/typesafe/sbt/packager/archetypes/JavaServerApplication.scala
index 7cebe30fb..0b79ea888 100644
--- a/src/main/scala/com/typesafe/sbt/packager/archetypes/JavaServerApplication.scala
+++ b/src/main/scala/com/typesafe/sbt/packager/archetypes/JavaServerApplication.scala
@@ -61,7 +61,7 @@ object JavaServerAppPackaging {
 
           for {
             s <- script.toSeq
-          } yield LinuxPackageMapping(Seq(s -> path)).withPerms(permissions)
+          } yield LinuxPackageMapping(Seq(s -> path)).withPerms(permissions).withConfig()
         },
       // TODO should we specify daemonGroup in configs?
       linuxPackageMappings in Debian <+= (normalizedName, defaultLinuxLogsLocation, target in Debian, daemonUser in Debian) map {