Currently, this problem is on nVidia GTX 600 series GPUs, and there's no concrete information other than what's posted below. TH is in the process of working on an article. This is a current validation issue with the SB-E CPU's and while the PCIe 3.0 support is on the SB-E nVidia called into question PCIe 3.0 support on the SB-E.
I truly wish I could give you better information, but this is all I have useful or not.
Here's a very good link ->
http://rog.asus.com/forum/showthread.php?11900-GeForce-GTX-680-Release-Driver-Limits-PCI-Express-to-Gen-2.0-on-X79-SNB-E-Systems
The SB-E has 40 primary PCIe lanes, 32 lanes of PCIe 3.0 are dedicated to the GPU(s), 8 lanes of PCIe 2.0 for chipset, all LGA 2011 CPUs & MOBO's are capable of PCIe 3.0, some BIOS upgrades have addressed PCIe 3.0 issues. Ditto the Z77 has the same 8 lanes of PCIe 2.0. All LGA 1155 including the IB have half the number of PCIe lanes to the GPU in comparison to LGA 2011; SB/LGA 1155 16 lanes of PCIe 2.0, IB/LGA 1155 16 lanes of PCIe 3.0 vs SB-E/IB-E/LGA 2011 32 lanes of PCIe 3.0
(subject to validations) to the GPUs then split in various ways.
Before with LGA 1156 e.g. P55 and LGA 1366 e.g. X58 the GPU(s) ran through the Chipset, but since Sandy Bridge LGA 1155 and Sandy Bridge Extreme LGA 2011 all GPU lanes are a direct path to the CPU to reduce 'latency.' Apparently, the 'issues' are limited to the LGA 2011 MOBO's
(BIOS Fix) and current SB-E CPUs.
Therefore, the SB-E running e.g. GTX 600 series or HD 7000 series GPU(s) is PCIe 3.0 clean *IF the drivers allow it.
The problem is with nVidia, the SB-E & AMD HD 7000 series runs PCIe 3.0 just fine. Yes, I've seen this ->
http://www.geforce.com/hardware/desktop-gpus/geforce-gtx-680/specifications
*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.
Registry fix (hack) to force the GTX 680 to run in PCIe 3.0 mode; see -
http://tinyurl.com/7awc9lv (RMPcieLinkSpeed, DWORD = 0004, etc. IMO - It's a bad act by nVidia...to Disable, if this is an issue on some LGA 2011 then the driver installer 'should' detect and notify the end user to rectify vs all LGA 2011 suffer from the few LGA 2011 with a BIOS issue.
Problem this might be ditto with the IB but Idon't know sine the IB CPU's aren't available nor any testing, since there's no difference in the PCIe 3.0 spec on either the SB-E or IB.
The HD 7000 series does run in PCIe 3.0 mode on LGA 2011.
You may also want to read -
http://www.techpowerup.com/162942/GeForce-GTX-680-Release-Driver-Limits-PCI-Express-to-Gen-2.0-on-X79-SNB-E-Systems.html
GeForce GTX 680 supports PCI Express 3.0. It operates properly within the SIG PCI Express Specification and has been validated on multiple upcoming PCI Express 3.0 platforms. Some motherboard manufacturers have released updated SBIOS to enable the Intel X79/SNB-E PCI Express 2.0 platform to run at up to 8GT/s bus speeds. NVIDIA is currently working to validate X79/SNB-E with GTX 680 at these speeds with the goal of enabling 8GT/s via a future software update. Until this validation is complete, the GTX 680 will operate at PCIE 2.0 speeds on X79/SNB-E-based motherboards with the latest web drivers.
Ivy Bridge and Z77 Chipset (Panther Point):
HD 7900 Series running PCIe 3.0 on SB-E:
GTX 600 Series running PCIe 3.0 on SB-E (fix applied):