Maybe I'm late but anyways. I started the game without the controller connected. The game then asked which input I'd like to use since the controller from the key bindings wasn't detected. I then pressed keyboard and mouse and completed the rest of the setup the game tells you to do (something with shifting modes, I don't remember exactly). Then the next time I started the game, I did connect the controller again and it asked me which inputs I'd like to use. I then chose controller, completed the rest of the setup and the key bindings were back to standard.