PCIe 3.0 is working on my X79 Classified. To make it work on both GPU's I had to move another PCIe card away from the port shared with the second GPU's port. In other words, neither card shares their bandwidth with any other card. I do not know if this is particular to my setup or not, or if it may be helpful to you or others, but I thought I would share it.

Best regards.

if it runs at 8gbs isnt it considered pcie3.0? i dont understand?

My friend uses this board ASUS Rampage IV Extreme and i threw my 670's in his pc and get pcie 3.0 no problem he has the same cpu as me.Looks like i should have stuck with asus brand this time.

There's more to it than a BIOS update - which was put out by Intel and not NVIDIA, BTW - or simply running Gen 3 speeds. And "PCIe 3 Ready" says that it can accept ver 3 hardware, but you must still have the ver 3 controller on the CPU or the PLEX no matter WHAT GPU-Z tells you in order to properly run and control the lanes.
 
And just look around at how many "They can do it but I can't" stories float around. Hard to ignore the possibility that what NVIDIA suggests might have some merit with that much happening.
 
Running PCIe 3 on hardware that's not designed for it - like the SBN-E with their ver 2 controllers - is nothing more than a straight-up "hack" in which nVidia chooses not to actively engage.
 
Sorry if that disappoints you in its reality, and that it doesn't sound as "involved" as some of the various "reasons" proffered by others equally disappointed...
 
 
EDIT:
Apologies for revisiting the subject, but the question of GPU-Z kept nagging me.
 
My system's straight-up X79, on an Intel DX79SI with an i7-3820 - the only SBN-E designed as an Extreme and not a Xeon derivative. I reset everything here to nominal stock so as to minimize sensor conflicts and put things into an easily-referenced starting point, then opened up several monitoring apps simultaneously.
 
Pretend it's a Geek version of "Where's Waldo" and see how many differences and discrepencies there are in this screen cap. The only info I will add is that my primary PCIe-x16 slot is locked at 16 lanes no matter its speed by design...
 

Well....Maybe mathew or Jacob could shed some light on this once and for all... is x79 pcie3.0 or not?

mack-attack Well....Maybe mathew or Jacob could shed some light on this once and for all... is x79 pcie3.0 or not?

Drop in an E5-1660, any of the E5-26xx, or next year's IBN-E and it will be...

The number of lanes assigned to the slot does not change with the power state, only its speed. What's on the left side of the GPU-Z readout is what's rigged while the left side shows what's running.
 
GPU-Z is showing the incorrect number of assigned lanes to my locked-in 16-lane slot...

Despite what your link has printed, I refer you to figure 1.1 (page 10), and especially section 1.2.2 (page 11) of the Series 2011 Datasheet, where it states:
 
"...Up to 40 lanes of PCI Express* interconnect for general purpose PCI Express devices capable of up to 8.0 GT/s speeds that are configurable for up to 10 independent ports..."
 
which means the chip can run up to 10 PCIe-x4 slots if so desired...