i had this problem when i 1st got my low profile gt220 but it was in a dell gx745sff with the hard drive less than a cm away from gpu so it was understandibl. but i solved it before by moving the hard drive to sit on a small shelf i made outside the pc for it and just leaving the case open.
it was working fine until about 2 days ago.
i upgraded my cpu to a core 2 e6400 which is running fine at around 40-50 degrees on the stock dell sff heatsink and fan
although after i had installed the cpu i got a start up error saying rear fan failure. and ive been looking around and it seems like the fan it means it the one that connects to underneeth the HDD....which ive never had to begin with.
after i got this error my gpu was idle at 50-60 and on load i saw it reach 111 degrees celcius then it shut down. before its idle was around 30-40 and load was 60-80. so i recently put new thermal grase on the gpu's heatsink (arctic silver 5) but still no difference.
ive double checked all the connections to my mobo and they all seem fine.