My Mountain Lion won't recognize USB controller button presses... Why?
I was having virtually the same problem and it turns out Chrome was the cause.

I'm using an Xbox 360 controller on Mountain Lion with the tattiebogle driver.  Recently, my controller would just cease to respond, even though it was showing as connected and no amount of disconnecting/re-connecting would fix the problem; the only thing that seemed to work was a re-boot.

I was doing some research earlier and came across this post.  I found it hard to believe that Chrome would be the cause, but sure enough, the controller has stopped working twice now and both times I closed down Chrome, re-connected, and all is fine again!  Thanks for your post, it helped me a lot!