Was the last version where your gamepad worked the previous beta or version 1.2.0? There have been some changes since 1.2.0 that I haven’t tested on Windows, so they might have introduced issues.
I can revert them if needed.
Also, have you tried connecting the gamepad before launching the game? That should work. It works fine for me - just tested it on Windows with a cheap no-name gamepad.
Good luck with your work - this project can obviously wait.