After a recent system update, my wireless Xbox 360 controller doesn't work anymore in Steam games. However, it does work anywhere else: in Wine games, RetroArch, MAME, I can even navigate in Steam Big Picture! It is the games launched from Steam that have this issue and I don't know what's wrong.
You can read the terminal output of Steam here (although I haven't found any errors about the controller specifically).
Edit: To be more specific, I use vanilla xpad (xboxdrv hasn't proved to be perfect in the past) and the affected games are DiRT Showdown, Overlord II, and Toki Tori 2+.