To me, it sounds like something is running either a system scan, or an update. You don't have scheduled virus scans or defrag sessions setup, do you? Or perhaps a daily check for updates on one of your other programs.
It could be heat related, but I would think that your symptoms would be more along the lines of the game freezing up on you completely.
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"Nein! I did not have sex with that fraulein"
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