I agree, its probley the thermal paste. I always replace that stuff myself now to make sure. It does not take much to increase the temp by 10 degrees though. I'm assuming one is not blowing air towards the other. I have 15x 5970s running now and they all pretty much run the same except having them sharing a motherboard is obviously going to cause one to get a lot hotter, taking in hot air from the other. I would say a 5 degree difference between actual cards is to be expected, but even that difference is probably linked to the paste to some degree.
You are correct, they are both side by side in separate rigs, drawing cool air from the back, blowing hot air into the center of the basement, no appreciable difference in their configuration/orientation. I looked around this forum for tips on replacing the thermal grease/paste and it looks like it's a matter of disassembling the heatsinks, remove old paste (scrape clean, swab with cleaner) and apply a small blob of expensive toothpaste then re-assemble. I could only find howto links for a CPU job:http://www.hardwaresecrets.com/article/How-To-Correctly-Apply-Thermal-Grease/274/1
Any pics, tricks to keep in mind? I'm good with hardware, but taking apart an otherwise functioning $300+ piece of hardware gives me pause.