Nvidia has released a patch that re-enables PCI-Express 3.0 speed on the GeForce 670, 680 and 690 graphics cards. When Nvidia introduced its GTX 680 card, the manufacturer switched back to PCI-Express 2.0 speeds, due to compatibility issues between the PCI-Express 3.0 controller of Intel's Sandy Bridge-E processors, and Nvidia's GK104 chip. A software update should fix the issue, as the new patch makes the GeForce 600 cards run at full speed once more on X79 motherboards.
The new LGA1155 'Ivy Bridge' processors also have a PCI-Express 3.0 controller, but were unaffected by the problem. The patch is only 380 kB and works only with the latest GeForce drivers for GTX 600 cards. Nvidia states it is unsure whether the patch completely fixes the issue, as it cannot guarantee the stability of the PCI-Express 3.0 connection between the graphics card and the Intel Sandy Bridge-E processors. The manufacturer advises against installing the patch on machines that are critical for business use. The patch can be removed easily by typing “force-enable-gen3.exe –revert” in a command shell. Nvidia's fix can be found here and should be used at your own risk.
PCI-Express 3.0 can be enabled again on X79 systems with a GeForce GTX 600 GPU