So, I've had both cards for about 2 years. They were water cooled for the past year until last night. The secondary card has always been hotter for some reason. I ran EVGA OC Scanner benchmark mode with each card separately and the primary card gets to 75c at the end of the benchmark and the secondary card gets to 89c. I've remounted at least 5 times within the past few days, and the temperature never changes, it's always at least 10c+ higher. I highly doubt it's a bad mount at this point. The hotter card idles at 45c while the cooler card idles at 41-42c both at 70% fan speed.
 
This happened when they were on water too. The second card was 63c under load while the primary card was 53c under load. It's starting to look like I have a bad card and may need to RMA it. Anyone have an advice before I RMA it?

What verison driver are you using? I got the same problem as your if you are use driver 301.42 so I sure their error driver on 301.42. When I using watch Win Tv and I notice the the card rise slow to hotter from 32 to about 45 to 48c n idle should be be about 35c or less!!! But other second card is fine normal drop temp when idle but first card still not drop temp. They both cards set temp at 32c idle when Win Tv off and on again so temp is back normal at 32c. This really strange and I sure the driver 301.42 got some bugs!!

Try checking the voltage on each card.
 
All three of my GTX 470s default to different voltages - 0.0938, 0.0950 and 0.1012 - in BIOS...

Both cards are 1.025v under load.

I get this as well on mine..
Under water as well. Can be anywhere from 10 - 15 degrees difference.
Idle it's ok but full f@h or gaming it changes.
Both set at same voltage.

Just one of those things I guess.

This is not in SLI though. Each card ran OC Scanner benchmark separately. Primary card finished the benchmark at 75c and my secondary card finished at 89-90c.

Have you tried swapping the cards position? My top card is always hotter regardless of which card it is. I am on water now so temp is only 1-2*C difference, but when I was on air it was about 10*C hotter.

Once again, this isn't in SLI, this is each card running separately.

Jpump


Once again, this isn't in SLI, this is each card running separately.

 
Doesn't matter SLI or not if both cards are installed at the same time. Try one card at a time instead of just disabling SLI unless that is what you already mean.