1. Current LGA-2011 CPUs officially do not have PCI-E 3.0 compatibility. So BIOS will not allow 3.0. Some MBs from other vendors have options to force 3.0 mode, but its untested, and PCI-SIG (maintainers of PCI specs) do not started official compliance testing for 3.0 level, as I know.
2. My Zalman case with 2.0 ports worked fine with DX79SI with case USB cable connected to MB connector marked as 'USB 2.0 front panel'. But front panel MB connector provide lines&power for only 2 USB devices. Your case have 4 ports on front, this means that kind of hub present, thus power line may become degraded.
THX JFFulcrum for your support
I have RMAed the board & got a new one. Which I will be installing today. I will keep you updated.
Logically speaking it should work as I have installed MBs before & left out the USB 3.0 front panel.
As for the the VGA card running in PCI 3.0 mode it should run without a hitch. The VGA specs clearly states that they are PCI 3.0 http://www.newegg.com/Product/Product.aspx?Item=N82E16814125437, so does the MB http://www.newegg.com/Product/Product.aspx?Item=N82E16813121534&Tpk=dx79si
I wonder why the GPUZ said that it was running in PCI 2.0, that is so weird.
I wonder where the good old days went, when someone could just mail Intel for support!!!!!
Just an update:
I have installed the new MB & everything works fine. Surely, I was disappointed by not having the PCI-E 3.0. Personally, speaking I think it was a scam & YES A scam by Intel.
I mean you go into the MB specs website & it says that it has 3 lanes of PCI-E 3.0 & you end up with PCI-E 2.0 is playing with words.
Moreover, everyone is annoyed by Intel's lack of support.