It's a slightly different engine, but you should be able to set the buttons again. Try doing so when Steam is not on.
I shut down steam, and it's still not working :/
Well, you should be able to set your buttons in the options menu button config -> joystick config.
... that's the issue... I can't. When I try to set anything to Pl, PR, L4, or R4, nothing happens, it stays blank. All the other input work, just not those 4 'extra' buttons on my controller.
Well shoot, I don't have a fix for that or even know what's wrong with it. Good luck with that controller.