Since release I've played with a Xbox 360 Controller and it worked perfectly. But somehow i can't use it anymore. I can't select any options in the menu and ingame everything except movement and camera is possible.
Be sure to make sure the drivers for your controller are up to date.
Secondly, verify the game files in the Uplay/Steam client.
Thirdly, please remove any non-essential USB peripherals that may be conflicting with the input.