I notice when I first apply power to my mobo, (plug psu cable into psu) the CPU fan would spin at full RPM, but when I turn the power on via the system switch it slows down and operates normally. I have another mobo of the exact same and when the system is turned off the fan stops as it should. It also goes to max rpm at the sleep state. Also Ive noticed the HD seems to be powered up as well, if I unplug the fan while the system is off I can hear the HD spinning, If I plug the CPU fan into the chassis fan header while off the fan doesnt spin. It seems to just be the CPU fan header and the HD that has power when it shouldn't.
I have isolated the mobo from the chassis just to see if theres something shorting and nothing is, still does it, everything is unplugged, updated BIOS and still does it.
First confirmed the BIOS was correctly loaded on the board, checking the BIOS version (should be ..86A.0125). if you have the correct BIOS, clear CMOS (it will set the BIOS defaults)removing the BIOS battery for 5 minutes then put it back, go to the BIOS and set the correct data and time and check results. I f you have a chance try other power supply or try that one in a tested good system to isolate the problem.