"Possible issue with the Steam overlay.
I had a similar issue and it had to do with Steam popping up an overlay to give me the CD key every time the game started. To see if this is the case, hold down the shift key while moving the mouse and see if that makes the cursor appear.
To make the problem go away, next time that little message popped up to give me the CD key, I checked a box telling it to not show me that anymore. Problem solved."
- http://forums.steampowered.com/forums/showthread.php?t=1772135