I sent a request to NVIDIA support about this issue a few months back but there has not been a resolution yet to the problem that I know of. I provided bug report logs as was requested at the time.
I use my Kepler 680 cards for compute purposes (CUDA/OpenCL) and the PCI-E bandwidth is very beneficial for this use. With driver 295.33, all my slots negotiate at 8 GT/s per Rev 3.0 spec with several different boards that I have which is working fine currently. Any drivers after 295.33 are capped at 5 GT/s as reported by lspci and nvidia-settings. I have tried all drivers up to 310.14 beta and all are limited to 5 GT/s.
Are there any plans to fix this issue? I would like to be able to upgrade my driver to a newer version at some point and this will be necessary if I am ever to buy any future released NVIDIA cards.
Thanks for your time.
Screenshots of nvidia-settings: