Intel says SB-E/X79 supports 8GT/s, but you'll notice that Intel doesn't say PCI-E 3.0 anywhere in its marketing or whitesheets on the processor and chipset. They didn't get the platform certified for PCI-E 3.0, so it either lacks some feature that PCI-SIG requires or they just didn't bother certifying it. Either way, there is no guarantee that PCI-E 3.0 devices will run at PCI-E 3.0 speeds, and that is no one's but Intel's fault.
Plus, I doubt there is really any performance lost from not using PCI-E 3.0, so who really cares?
Rig1: System Specs.
Rig2: A8-5600K@4.4GHz / AsRock FM2A75 Pro4 / 8GB Corsair DDR3-1600 9-9-9-24 / HD7560D / Samsung DVD-Burner / 1.5TB WD Green + 3x3TB WD RED in RAID5
Rig3: Athlon X2 4200+ / M4A79 Deluxe / 4GB G.Skill Pi DDR2-800 4-4-4-12 / GT430 / Sony DVD-Burner / 500GB WD
Rig4: Phenom II x6 1605T @ 3.6GHz / Asus M5A99X Evo / 8GB PNY DDR3-1600 9-9-9 / GTX470 & GTX470 / Samsung DVD-Burner / 1.5TB Seagate