My similar experience : Mac pro 4,1, upgraded 5,1 under 10.8.3, with w3690 + evga gtx 670 2Gb. Evrything run smoothly untill 2 days ago, without any notice (as far as i know, no system upgrade. PCI-e fan always at 800 rpm, and now around 1500-1600 rpm. Pushing with a gpu intensive application at 2000 rpm has the effect to unlock this high fan speed, otherwise it is stuck to 1500 rpm and never lower !
I did pram reste --> no effect. I did smc reset, twice, no effect ! I have my system backup on a external drive. I noticed that at the first boot on this backup disk on FW, the fan speeds are all OK around 800 rpm (booster and PCI the others at 600 rpm). But the next boot the PCI fan speed goes back to 1500 rpm.
Very strange ! I do not see a cause to this. For me it is not a Hardware change and I do not think it is a hardware failure wether the graphic card nor the computer or internal components I have in (6 SSD + 4 HD + 2 velocity solo x2, + 1 esata card).
So i suspect is is software, but i do not have the courage to test another osx version startup disk ...