After trying to create a custom keyboard layout for Old English, my Shift, Ctrl, Alt, and Super keys stopped working outside Discord and a few other applications. I can't use shortcuts like Ctrl+A, and even pressing Enter in the terminal does nothing. The keyboard tester in system settings detects the key presses, but the desktop environment and several applications don't seem to respond to them. I'm running Bazzite with an NVIDIA GPU. I deleted the custom layout and switched back to the US layout, but the problem remains. Any ideas what configuration might be causing this?
2 Answers
This sounds like a user-session configuration problem, possibly a global keybinding or input-method setting left behind by the custom layout. Since the key tester sees the physical presses, the keyboard hardware is probably fine. Checking whether you’re using Wayland or X11 and reviewing desktop keyboard shortcuts would be useful first steps.
A quick way to confirm whether your personal configuration is broken is to create a temporary user and test the keyboard there. If the modifier keys work normally in the new account, the problem is limited to the original user’s settings rather than the system or keyboard. In that case, you can migrate your files and recreate the affected desktop or input settings.
Creating a new user fixed it. I’m going to transfer my files over and use that account, since something in the old user’s configuration must have been corrupted.

I’m using Bazzite, but I’m not sure whether my session is Wayland or X11. The issue affects the desktop environment too, not just one application.