I have some issues with rivia tuner and fan speeds my self. I doesnt like staying at much over 80%. I normally settle for 60% and it seems to stay at that giving me time to play with overclocking etc.
Do you have the latest version of riva tuner and drivers ? What card you using?
Maybe its a built in feature of the card to deduce the fan speed back to auto after a period of time if the gpu usage drops.