I got the same thing in device manager (0000002) yet I'm starting to wonder how accurate these numbers are. HWiNFO64 shows my GTX 1080 running on version 3.0 while the device manager is showing value 00000002. The same program, of course, shows 2.0 for the WiGig card no matter where I put it and of course 00000002 in the device manager.
I also had the WiGig card in the same slot which shows version 3.0 for the video card currently.
BIOS is set from Auto to Gen3 now.
I'm starting to wonder if the BIOS won't run this card on Gen3 because it's not a video card or it won't run two devices on gen3 at the same time. Or it's running on Gen3 but being shown in windows incorrectly as Gen2. Lastly, maybe the PCI Express lane speed doesn't even matter and something else is the bottleknock. Or this card runs as Gen2 only.