I'm using a PS4 controller and all of the control graphics are just white squares. The PC controls show up correctly. Initially all of the controls were shown as XBox controls. I tried deleting all of the files and reinstalling but it hasn't fixed it.

i'm having the exact same issue, PS4 controller as well, but i've never even got the 360 buttons to show up, just big white squares and PC buttons. your post is the only other person i can find reporting this issue.

Thank you for reporting. The game is trying to intelligently show you PS4 buttons but I guess I didn't test it enough. I will try and patch it in the next version.