OK so I can't seem to figure this one out. While I was going through the BIOS I noticed my GPU is running in Gen 3 x8 not x16. I looked through the manual and for my 7820x I have 28 lanes available with this motherboard, I have my GPU plugged into PE2 and in the manual it says it should have x16 lanes from CPU, I have also an 80mm key-m m.2 nvme ssd in the slot below PE2 and that according to the manual only takes 4 lanes from CPU and I have under the I/O shield a Key-E 32mm wifi card that takes 1 lane from PCH.... Yet even with leftover lanes for the cpu I still cant get my GPU (an EVGA 2070 xc) to run in anything but Gen 3 x8
 
I have updated my bios to the most recent 1.28
I have cross referenced this with GPUz and it also shows Gen 3 at x8 even under load
As a Last ditch effort I also reinstalled windows and reset the bios, same issue, no change.

Can anyone help? I have searched all over but can not find a solution. 
 
Edit: If someone would like to see if maybe I just missed something here is a link to the Manual, https://www.evga.com/supp.../files/142-SX-E297.pdf
 
Edit: here is GPUz screenshot
 

I'm not sure where you are seeing that PE2 is an x16 lane slot, it is x8 for both 44 lane and 28 lane CPUs.
 
From manual for 7820x:
PE1 x16 (x8 if PE2 is occupied)
PE2 x8
PE4 x8
PE5 x4
PE6 x4 (if M.2 is disabled)

Well thanks for the help I'm not sure what the issue was exactly.. A bug maybe? I toggled the bios chip selector, it wouldn't post or boot just kept beeping with no screen signal, then I turned it off and toggled back to the removeable chip and now it sees it as x16 gen 3.... I had tried reseating everything, cleaning contacts, reinstalling, reflashing, everything I could think of. 

Hopefully this doesn't mean my bios chip is getting ready to fail. 

the_Scarlet_one

DEJ915
I'm not sure where you are seeing that PE2 is an x16 lane slot, it is x8 for both 44 lane and 28 lane CPUs.
 
From manual for 7820x:
PE1 x16 (x8 if PE2 is occupied)
PE2 x8
PE4 x8
PE5 x4
PE6 x4 (if M.2 is disabled)

You are most likely reading the wrong manual, because PE1 on the FTW K is very much not an x16 lane, meaning you are in the wrong manual.

Yep, just looked through all of the manuals, and you are looking at the x99 FTW K rather than the x299 FTW K. Those boards are very different.

No I misread and thought they were talking about the Dark board, you can disregard my post.