*Bump* Please, I would really like to get this resolved.
Do you know what revision your motherboard is? v1, v3 or v3.1?
The two updated GIGABYTE boards have a UEFI bios. The older model has a legacy (AMI) BIOS.
From what I've seen, problems like this are usually a conflict with the UEFI vBIOS found on the video card and the legacy BIOS on the board.
The card should work normally once you boot into Windows.
A handful of MSI cards have a Dual BIOS switch - have a look for that:
Your GIGABYTE board may have an option to force PCIE ports to Gen 2 - if your board has such an option I'd try that also.
Other than that you might be stuck.
I picked up a Sapphire card myself as they have a dual legacy & uefi vbios.
My old ASUS M4A785TD-V EVO seems to have no trouble with either mode.
Thanks for taking the time to compile such a list, I have gone through and checked each variable.
My Mother board is rev 1.0, but in system summary it tells me my BIOS mode is UEFI and running the latest version F12, and according to the MSI GPU Bios it is all Hybrid and up to date also.
It's a strange one. will keep an eye on those other posts and see if any one else can figure it out. Doesn't seem to be effecting any thing else in the PC. although, I'm not sure if it's related, but trying to watch anything on Youtube causes my monitor to turn Black (or Green sometimes) and the whole computer freezes up, forcing me to restart. I heard that could be GPU related maybe.
Unplug the graphic cards, than plug it again.. Boom