Breaking gamepad controls

So, I really enjoyed the gamepad controls so far on my laptop (even though they have some quirks) and yesterday I decided to play the game on my pc. I copied my safe files over and started the game. Saves were there, no problem.
But, I somehow couldn’t use my gamepad the way as on my laptop. So I checked the controller configuration and most actions didn’t have any buttons assigned to them.
So I went ahead and did that manually. As soon as I had assigned the ‘A’ button for one of the guns, I regretted it. Somehow I can’t use my ‘A’ button anymore to confirm choices in the menu, meaning the gamepad is basically useless.
Well, I thought to myself, let’s fix that. But somehow I can’t get it fixed.
I tried restoring default configurations without gamepad plugged in, reinstalling the entire game, reinstalling gamepad drivers, restarting my pc, deleting the Sunless Skies files in LocalLow.
Nothing worked so far. The configuration for the gamepad stayed the same. Which is really bugging me. Where is that information stored.

Does anyone have an idea what else I might try?
I already have a bug report ready for submitting, but I thought if anyone had a quick idea for a fix, I might give that a shot and then include it in the bug report.
FYI, I am on Windows 10.