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Have you looked under the fan settings in BIOS ? I dont remember exactly what its called on your board but i think they have some kind of "Smart" fan control that controls fan speed according to CPU temperature - maybe thats your problem.
Other than that you could have a bad fan header - if thats the problem you could get a 3-4 pin converter so you can plug your CPU fan into a molex plug (like the ones used on HDDs) - these converters even come with the extra wire and plug you can plug into your motherboard header so the RPMs can still be monitored - but the fan gets the full 12V from the PSU.
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