I have been facing this fan problem lately. Whenever i start any game(say battlefield bad company 2), the fans(two) speed get too high and the game gets slow after a few minutes of gameplay. FPS drops down. I wasn't facing this issue before. Its just now that i have been facing it.
My system specs
AMD phenom 2 x4 245 @ 3ghz(using stock fan)
Asus M2N68 +
4 gb ram
Nvidia GTS 250 1 GB
Windows XP service pack 3(32 bit)
Sorry, I am a noob at these things.
I just got one extra fan and a heart sink(stock one). I don't know which fan gets too high. I can hear the noise very loud while playing games.
And yea...My normal CPU temperature is 47 degrees. And while playing it rises to 61 degrees and the fan speed gets high from 4066 RPM to 5351 RPM(while gaming).
It sounds like your GPU is overheating and since the cooler is clean then there are only two things you can do; if under warranty RMA, if not take the cooler of clean old thermal paste off and reapply with new.