Thanks for the compliments! Someone else was having the same problem, but then the other way around. Can you tell us what controller you have, on which OS?
I used the controller Thrustmaster Dual Analgo 4 ; it's a ripoff of the Xbox controller but with all the button twisted , I played on Ubuntu 14.04
Hmm, that's quite an exotic combination :). We're using Rewired, which supports a lot of controllers. Unfortunately, not all controllers are known to be 100% compatible with every system. We'll update to a new version in the near future, hoping that that fixes it.