I ran into a bug today on the current Steam version (1.0.4) which I think might be caused by the beta controller support. Keyboard commands refused to work unless I pressed the key at least twice in a row. I disconnected my controller and the problem immediately went away; I didn't need to restart the game or anything. If it helps, I'm running Windows 10 and my controller is a DS3 which I'm using via a program called Scarlet Crush.