I have found that when running SLI or CrossFire that the two (2) cards Always run at different temperatures underload. This difference in temperature is generally 10C to 15C.
This is true in each of these example system I own:
- Corsair 800D case, dual Sapphire Vapor-X 5870's
- Antec P183 case, dual Sapphire Vapor-X 5770's
- Lain Li case, dual Sapphire Vapor-X 5770's (just tried this out, then moved 'em back to the Antec case)
- HAF-X case, side and two top 230mm fans, one front 200mm fan, MSI Talon Attack GTX460's
The ONLY solution I found that reduces this temperature difference between cards it to have a motherboard which allows the two cards to be separated by three (3) open slots. In this example I have one card in the Blue PCI-E closest to the CPU. And the second GPU in the White PCI-E slot, 3 open slots away....
http://www.newegg.com/Product/Product.aspx?Item=N82E16813131614
Using both Dark Blue PCI-E's, with single open slot between them one card runs Hotter.
I also have this MB with two (2) open slots between cards, same thing one card runs Hotter. And its in the HAF-X case so the ventilation is as good as it could possibly get....
http://www.newegg.com/Product/Product.aspx?Item=N82E16813131403R
So, yes, in my experience a temperature difference between cards in SLI or Crossfire under load is NORMAL....