Hey I'm getting the same issue on Mac. Downloaded the humble bundle version of the game.
Using a PS4 controller. It is very glitched out. left and right d-pads work but they move the character up and down. Up and down d-pad controls don't work at all. Left thumbstick only works in 1 direction. Right thumbstick does nothing.
After messing with the menu controls (I think this is what caused it), I was able to move my character left and right but using the up and down d-pad buttons. Left and right d-pad stopped working. Not sure what's going on here.