I know a lot of people seem to be using a 360 controller for this game, I'm using a generic brand one. So the game detects the controller just fine, but there's a lot of controls I want to reconfigure. I went through the joystick controls section and remapped everything, but the new controls don't seem to take. It isn't saving the new configuration, even though when I quit and come back it seems to have saved my new controls on the settings screen.

Anyone have any suggestions?

If you installed the game in Program files folder, try to reinstall it to another location, like C:\GOG Games

That's where it is saved. I tried changing compatibility and all that, like people suggested in a similar thread. Let's see if that does anything.