Major visual fighting for windows to "be on top"

[Mycheze]

When running the program, there can only ever be one MTGO window on a monitor, and it's always on top. If there are two open, they flicker back and forth. I always have anything I'm not using minimized. In the same vein, any other programs are always "forced below." For example, I take screenshots of my decks, which opens a "save the file" window, but that gets put under MTGO and I need to do some Alt+Tab speed tricks to grab the window and drag it to the other monitor.

Recorded a video example: https://youtu.be/sEYV3rPJ4TM

This isn't a huge problem since I can just minimize things, but it'd be nice not to worry about.

OS: Pop!_OS
Desktop environment (for Linux): Gnome
Graphics card: NVIDIA GeForce RTX 3060
Output of docker info:

Client: Docker Engine - Community
 Version:    24.0.6
 Context:    default
 Debug Mode: false
 Plugins:
  buildx: Docker Buildx (Docker Inc.)
    Version:  v0.11.2
    Path:     /usr/libexec/docker/cli-plugins/docker-buildx
  compose: Docker Compose (Docker Inc.)
    Version:  v2.21.0
    Path:     /usr/libexec/docker/cli-plugins/docker-compose

Server:
 Containers: 4
  Running: 1
  Paused: 0
  Stopped: 3
 Images: 5
 Server Version: 24.0.6
 Storage Driver: overlay2
  Backing Filesystem: extfs
  Supports d_type: true
  Using metacopy: false
  Native Overlay Diff: true
  userxattr: false
 Logging Driver: json-file
 Cgroup Driver: systemd
 Cgroup Version: 2
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
 Swarm: inactive
 Runtimes: io.containerd.runc.v2 runc
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 61f9fd88f79f081d64d6fa3bb1a0dc71ec870523
 runc version: v1.1.9-0-gccaecfc
 init version: de40ad0
 Security Options:
  apparmor
  seccomp
   Profile: builtin
  cgroupns
 Kernel Version: 6.4.6-76060406-generic
 Operating System: Pop!_OS 22.04 LTS
 OSType: linux
 Architecture: x86_64
 CPUs: 12
 Total Memory: 31.22GiB
 Name: pop-os
 ID: 8ad9488a-c95c-46ae-94fc-46cea79cec09
 Docker Root Dir: /var/lib/docker
 Debug Mode: false
 Experimental: false
 Insecure Registries:
  127.0.0.0/8
 Live Restore Enabled: false

output.log

[pauleve]

Is it happening with desktop emulation enabled as well? You can activate it using `./run-mtgo --winecfg > Graphics:

[dorianbrown]

Not sure if this would be the same as Mycheze's answer, but for me enabling virtual desktop does prevent the windows from fighting to be on top (both within the desktop and between the virtual desktop and other linux windows).

I wouldn't consider this to be a real fix though, since it prevents alt-tabbing between the mtgo windows, but hopefully it helps with figuring out what's happening