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)