Also have been having a significant heat variance between Card 1 and Card 2. The motherboard I am running is the Gigabyte X58A-UD3R. I have both cards sitting in the PCI-E x16 slots which means the cards are pretty much on top of each other.
GPU 1 runs under load between 88-94 celcius and GPU 1 is generally 50-60 celcius. I have the fans on both cards manually running @ 95% to ensure the temps on GPU dont get out of control.
As an FYI the case use is the Antec 900 with additional 120mm fan. Any thoughts? Is it worth switch card 2 into the x8 PCI-E slot for that bit of added room between the 2?
This is nothing new, the only real way to bring down those temps is to pump much more air between both cards quickly enough so that it doesn't recirculate. I was forced to add to 40mm fans that literally mounted on the pcb of the card below with the other being made to mount on a bracket. One to bring fresh cool air in and the other to bring out the hot air. It dropped temps of both cards nicely enough to removed the hot spot from the rest of system.