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I don't know... I never had this problem. I've left my Mini running for several days without any issues. You use Boot Camp, I assume? Then shouldn't that CD you had to write when you first set up Windows have some sort of app to control the fan speed? Or maybe your fan's broken? Or perhaps, if you've ever opened your Mini, you unplugged the fan connector (the little wire in the front), and forgot to plug it in again?
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