@malcolmlewis I have some more information on this.
I’ve done multiple fresh VM installs using Agama, and the issue is 100% reproducible. However, it seems to be locale specific.
If I have both the Gnome system language and the keyboard layout set to English US, everything works as it should. If either of those two is set to Slovak and the system is reboot, the bug starts appearing 100% of the time.
The easiest way to break an en-US system installation is to open the Gnome settings, go to the keyboard tab, add Slovak layout as an input source, delete all other layouts and restart the computer (note this is important, otherwise the keyboard layout will change but the bug won’t appear).
After the restart, I can no longer focus VLC, I usually for testing purposes am opening it from Gnome Console, but I suppose this does not matter.
I’m testing with the screenreader turned on both on the login screen and in the environment. I’m not sure what’s the relation between Orca and this bug if there’s any, since it’s hard for me to debug without a screenreader, I once tested this by blind booting the VM without the screenreader launched and starting VLC, afterwards I took a screenshot and GPT 4O reported the VLC window was visible, this was with the Slovak interface and layout. So there could be a connection, but I can definitely say with turned on screenreader, the VLc window is not focusable if either the system language or the keyboard layout is Slovak.
@ferdy81 do you use a localized version of the system? Have you tried launching with Orca? Other apps than VLC and KeePassXC, particularly Thunderbird and the Gnome Console / Terminal work fine for me, but since the system is unusable for me in this state because I need the password manager, I didn’t test many apps, so indeed VLC and KeePassXC being both QT may be just a coincidence.