While technically this is a plugins problem (and should be moved to plugins) I'll try to answer it. I had the exact same problem. When N-Rage's plugin queries for devices, it populates the list of controllers based on a fixed list of what it considers "acceptable" instead of simply querying for a list of game controllers. If your gamepad happens to return its subtype instead of its type (i.e. mine reports itself as a flight stick) then N-Rage won't add it to the list.
Since I don't have my joystick here at work I can't test the version I just compiled, but please tell me if this version picks up your joystick.
Also, please ONLY download this fix if you're having trouble picking up your joystick (or you enjoy testing alpha software). Please don't distribute this file.