I tried a few different gamepads on this game (xbox 360 gamepad, steam controller, 8bitdo sn30 pro+, nintendo switch pro controller, 8bitdo n30 pro2) and the only thing that got my controller working was unplugging and replugging my mouse/keyboard.
just start up the game (gamepad connected) and it's not responding. disconnect mouse/keyboard -> gamepad works from now on.