San Pedro said:
Scan for virus, and get spybot search and destroy to scan for spyware.
It sounds like something is running in the background that is taking up CPU or RAM.
Or a memory leak? But I never heard of a memory leak in CS 1.6.
Also the Llama has a point, do you play any other games? If so then are you getting similar problems? If not then the re-install idea is one of your best bets.