What software you have running in the background? Virus scanners, P2P software and their ilk should not be running when you want to play the game - otherwise, the system performance will be impaired and subsequently you will experience what you describe.
Also, the same thing might be caused by the "throttling" feature most modern CPU's have to prevent overheating - if your CPU overheats, it is likely that it will start throttling. You might want to clean out the radiators and fans.
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