Hi there! I have had the same problem earlier with my EVGA 8800 GTS, but I think I found a way to fix it:
This downloads You a prgram, that let's You modify some things with Your nVidia VGA.
sudo apt-get install nvclock
After it has ended, type
This brings the fan to 'Auto' speed, depending on the actual temperature of the GPU. If it were not enough, You can change the "auto" part to a number 25-99, as "fan speed in %"
sudo nvclock -f -F auto
After it seems to be OK, You have to manage to run this every time the computer starts. So You have to put in the auto-starting sessions.
System->Options->Sessions (Or something like that, I use a hungarian version)
I hope this helps! Bye!