Just wanted to give a heads up that there are some known issues with different controllers at the moment. Currently the xbox 360 controller is well supported, but other controllers may experience some weirdness. I'm currently completely replacing the game's input system to provide better automatic mapping to different controller schemes. Once I've given it a good amount of testing, I'll push the fix out. You'll lose any custom keybinds at that point, but otherwise the fix should be relatively seemless, and should be out some time this weekend if all goes well.
-Sean