i used to have the same problem on my new rig. i would play a game and when i tabed out or quit i would have to hit alt+ctrl+del and then cancel out and it would all come back. Took me awhile before i relized i needed to upgrade the video drivers , and then it went away. Have you tried that?
Sounds like some sort of a windows corruption. If it's only happening when you come out of counter strike then try reinstalling CS, if it's happening coming out of other programs, then reinstall windows.