Like the others have already mentioned, this type of card just blows the hot air from the graphics card around your computer case. A reference designed 7970 with a blower fan is quite loud, but gets the job done in displacing the heat produced by the card. Another consideration (which I currently use) is to get a full card waterblock (universal blocks do not cool 7970 mosfets, so the board will crash in minutes at high clocks under load).
I agree, but this doesn't seem to account for the problem the OP is having. Placing each card individually in his rig still results in one card running at much higher temps than the other.
I would avoid this design from the start. Apparently since they aren't reference, they also change the voltages as they please to achieve their meager overclock.
In my experience, reference design is always a superior solution.