They have a mode switch for the joysticks, add a button or jump it with a screwdriver, see if that helps
https://forums.cdn.launchbox.gg/monthly_2025_05/71CW7oJxhhL._SL1491_.thumb.jpg.2d8406720759410ee8709e9f8b5c2658.jpg
I downloaded the CLI version (it's just the exe) , put it in the main folder with the qtlauncher exe and pointed launchbox to that. It fixed the full screen issue also. I set a gamepad combo in the launcher to quit (under hotkeys if I remember correctly)
Ok that makes sense, the confusion comes from expecting it to be like the region or media priority tabs. On closer look it seems that eveything thats been played (regardless of playtime) is marked as active on the update which was the other thing that was throwing me.