So I took a break from playing the game for a few months and decided to come back to it today. I noticed that now the inputs when I use a controller are messed up, such as double inputs when I use the directional pad and weird accelerations with the analog sticks. It looks like the game is trying to switch back and forth between my keyboard and the controller. Is anyone else having this issue? This was never an issue with GOG until now. And everything works perfectly fine on the Steam version.

I bought the game yesterday and decided to play it today. Experienced the same issue. I solved it by making sure to not have Steam or any other program that uses the controller running in the background. Everything works fine.