Strange, never heard of a case where the stick works and the buttons don't. A few questions:
- Are you using an official Sony-branded controller?
- Are you using the Sixaxis app?
- In the mapping screen (Settings->Input->Controller), do the button icons turn blue when you press the physical button they're mapped to?
- In the controller diagnostics screen (Settings->Input->Controller->(menu)->Controller diagnostics), are button presses detected?
- What happens when you use the built-in PS3 input profile (can be loaded from the mapping screen)?