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MSI 7970 not detected in PCI-E slot #1, is detected in #2 Maximus IV Gene-Z

Level 8
Here's one I couldn't solve myself.

I've got a Gene-Z and it doesn't have any issues.
However, when I plug in a reference model MSI HD7970 it doesn't get detected in slot #1.
It does get detected in slot #2, but it's limited to PCI-E x8 v1.1 (not v2.0).
Both PCI-E slots work fine with a GTX 560 Ti, nothing changes after resetting the UEFI settings.
Bios version is 3603 (latest afaik).

I've been using the HD 7970 for the past three months and haven't had any issues as of yet, not even in surround gaming 4320x900. Performance is as it should be according to benchmarks I've done.
Since I'm thinking of buying another used HD 7970 or 280X for CrossFire I need to fix the detection problem first.

I'm thinking that the graphic card's BIOS should be updated, but it could be something else.
What do you guys think?

Here are some screens with specs and version numbers.


Level 8
Quick update:
Just noticed that the bus interface changes from x8 v1.1 to x8 v2.0 when gaming. I guess that's a way to save power.

But still, I can't get it to detect in the other slot as x16.

Level 9
I forget the name of the setting in the BIOS, but try changing the PCIe to prefer Legacy option rom. Something like that.

Intel do not support sandy bridge for UEFI

Legacy is better anyway, the mouse works in Bootmanagers and the legacy video bios in even current video cards is probably more tried and tested over the last 10 years. UEFI is new for the rapid boot thing, it pre-guesses settings and feeds them to windows 8/10, but things like mouse drivers don't seem to be stable and Sandy Bridge iGPU has no BIOS ROM/driver.

p.s. never change the PCIe video option from auto-detect. For example, if you set it to iGPU in UEFI then the BIOS loads the iGPU but windows steals it and loads the dGPU using iGPU memory, which results in weirdness.