Two I use on OS X are KeyRemap4MacBook and Spark. ControllerMate is excellent as well (I used to use it to program my Nostromo N52 gaming keyboard), but it's not free and has a steep(ish) learning curve, imo.
Check your keyboard shortcuts in System Preferences. Alternatively, download something like Spark and create your own shortcuts. I use it to map shortcuts to remote AFP shares and remote desktops on the fly.
I've not had this issue, though I did find they interfered with Controllermate which was a complete PITA because I was hoping to use that to replicate Autohotkey (instead, I use Spark for simple text placement).
I didn't realise it was that simple to change the buttons.