Hi. I recently changed my ASRock M3N78D-FX with the 990FX Extreme3 motherboard. But when I turned the PC on, the GPU fan after starting quietly at 40% at most, steadily got up to 60% for no reason - even if I stay at the BIOS it would go up in two minutes no matter what. I thought the heat-sink may be clogged but after I cleaned the little dust that has accumulated, the result was the same. I even changed the thermal grease but there was no difference. This was not observed on the M3N78D-FX mobo (with no load the GPU fan stayed at ~43% at most) and right now I am in doubt whether I should return the new mobo in the legal 7-day period in my country and buy something else.
With no excessive demand, the fan should come right up to the speed it is going to run at immediately. It shouldn't slowly ramp up over minutes. If this didn't happen with a previous MB, you can assume it isn't the card. I would return the MB.