XBox360 controller not working

I recently got a new 360 controller, and it works just fine in other games. In Portal 2, I enabled it through the settings menu, and it now works perfectly fine for menu navigation, but nothing else.

I can use the left stick to navigate, A to select, B to go back, even press the Start button to go into the menu; but I can't move or shoot portals or do anything.

Are there any known fixes for this?

Thanks!

XBox360 controller not working