Maybe you can help me. I kinda have a similar problem. I got a generic controller to work first then tried to get a 360 controller working. The 360 works in Emulation Station, but not the emulators themselves. When I load the emulators, it looks like they are seeing the generic controller as port 0 and the xbox controller as port 1 and therefore not responding to the xbox controller.
Any idea how to remove the generic controller?