PCI-E 2.0 shouldn't make a difference. I have to double check the manual, but it may be that the white PCI-E slot is fed from the south-bridge, such that data between the two cards has to transfer over the hyper-transport link.

Still, I don't think this matters, as on my system I score 18,300 on 3DMark and performance in games is equal or better to what they were on the 680i using the same components.