TechPowerUp points out that NVIDIA has decided against implementing PCI Express 3.0 support for its GeForce GTX 680 on Intel X79 based motherboards with Sandy Bridge-E processors.
Pre-launch drivers, including the driver that ships on discs with the graphics cards, and review drivers (which cannot be distributed), will let the GPU run at Gen 3.0 mode on some X79/SNB-E systems, however the post-launch stable drivers (such as GeForce 301.10 WHQL), won't.
The specifications page of GeForce GTX 680 on GeForce.com has been updated to mention this:
GeForce GTX 680 supports PCI Express 3.0. The Intel X79/SNB-E PCI Express 2.0 platform is only currently supported up to 5GT/s (PCIE 2.0) bus speeds even though some motherboard manufacturers have enabled higher 8GT/s speeds.
It seems that at least for now, Kepler will only run in PCI Express 3.0 mode on Intel's upcoming Ivy Bridge platform. TPU speculates this may be due to a discrepancy with validation, and that PCI Express 3.0 drivers may follow when NVIDIA is 100 percent sure that its Gen 3.0 mode will work with Sandy Bridge-E. The impact on performance should be non-existant though when using a single card, only in x8 when running SLI could it bottleneck your graphics performance.