Phantom PCIE device?

[sinspiren]

Hi guys, I am really out of idea now, basically my 3080 would not run at x16 no matter what, I was fine before I install a water block on it.

 

My setup:

CPU:6800k and Xeon 2620 V3

GPU:3080 

Motherboard: Asus X99 A-ii

Power supply:Corsair AX860I

 

So far the trouble shooting I did

 

1. Clean/Reseated the gpu, pcie slot. multiple time.

2.Tried another CPU (Xeon cpu, so pcie lane shouldn't be a problem)

3.Swapped power cable.

4.Looked at bios. Reflash the latest bios, Clear CMOS.

5.When using  Xeon 2620 V3, tried all other slot, still showing x8 at any slot

 

So far, when I went into bios, it shows my gpu is running at x8, before even loading the system, so it should not be a windows/driver related issue.

I am using an 6800k (28pcie lane), gpu in the first slot, no other devices in pcie slots. From the the PCIE lane illustration, the only time slot 1 going to be x8 is when slot 4 plugged in, Now the interesting things happens, when I actually plug in a x4 PCIE NVME ssd in to slot 4, the bios report my graphics card in slot 1 is running at x4. Much like there is another pcie device hidden somewhere. But in bios, I don't find anything seems related, not sure if it is relevant at all, but I also tried to complete disable SATA, STATA express, USB3.1. DMI, but non of them helped.

 

I do have a M.2 NVME as system drive, directly put in the M.2 Slot,  but looks like it is independent from the PCIE slots, and it was fine even few days ago, so I doubt it is the problem

 

I don't have another GPU or mother board to test out, but I think neither is for blame, well at least hardware level. The motherboard did it once though in the past where it shows the exactly same problem when I had a GTX 1080, but it was solved by reseating. 

 

REALLY out of ideas now...help please!

 

MOBO PCIE lane break down:

When 28lane CPU installed: https://techreport.com/r.x/2016_7_30_Asus_X99A_II_motherboard_reviewed/06-diagram_pcie_routing_28lane.gif

When 40lane CPU installed: https://techreport.com/r.x/2016_7_30_Asus_X99A_II_motherboard_reviewed/07-diagram_pcie_routing_40lane.gif