It sounds to me like Q-Fan/Smart Fan, which is probably enabled in the BIOS, if it is doing this in windows.
This usually happens when the processor or case temperature is very near the ramp-up threshold. The fans spin up, reducing the temperature beneath the threshold, and then it slowly climbs back up, causing them to spin up and repeat.
Either try to improve ventilation, reseat your HSF w/ Artic silver, or download fan management software and change your thresholds.
And once a harddrive has "spun up" to its RPM (i.e. 7200RPM), it does not vary in speed during normal operation.
If you mean the computer won't boot up at all, and the fans go fast like normal, then slow down, and repeat and equal intervals, then you have a different problem. Do you have both power connectors plugged into the motherboard?