Damn :( sorry to hear that, I don't have a linux install so I don't usually get to test the linux build, just hope that it works...
So here's what I did, I updated the controller thingie I use (It's called Rewired, for Unity). So try downloading 1.4.5 and please let me know if the problem was solved.
The second thing I did was cross-posting what you posted here in the Unity Rewired Forums, to see if the creator of Rewired knows anything about this. Here's the link to my post: http://forum.unity3d.com/threads/rewired-advanced-...
Welp, thanks for letting me know of the problem ^^