@jonasdanys - Then loaded optimized default?? How and where are you checking HPET is enabled or not?

I checked your BIOS region dump, all 100% disabled now, there is no way this is enabled at the BIOS level.
Here's my notes as I extracted and double checked all previous changes, and checked for anything new in full NVRAM dumps that may need edited

Hello,thanks for the help (ye hpet off). It took me a while to realize that mobo runs gpu x4 3.0 speed at x16 slot. I tried another motherboard and another one works great. it's a defect or something i can do?
i tried f5,f6,f9,f10b bios... and gpu drivers latest
GPU: 1080 ftw2
Mobo: Aorus ultra z390

btw x8 slot works great.
gpu-z

cpu-z:


Bios photo:

@jonasdanys - Maybe power save feature, click that checkmark and run 3D test, see if it increased from x4 to x16. if not, it may be the card itself is only x4, or you are sharing that slot with another card you have installed, or maybe shared PCIE Lanes with M.2 slots? Check manual about that, it will tell you
Yes, I see you have two x4 M.2 NVME installed, and one of the slots on your board is 16 length but only x4 electrical + specs below (See manual for more details on which slots are affected by M.2/NVME installations etc)
https://www.gigabyte.com/Motherboard/Z39...#support-manual

1 x PCI Express x16 slot, running at x16 (PCIEX16)
* For optimum performance, if only one PCI Express graphics card is to be installed, be sure to install it in the PCIEX16 slot.
1 x PCI Express x16 slot, running at x8 (PCIEX8)
* The PCIEX8 slot shares bandwidth with the PCIEX16 slot. When the PCIEX8 slot is populated, the PCIEX16 slot operates at up to x8 mode.
1 x PCI Express x16 slot, running at x4 (PCIEX4)
* The PCIEX4 slot shares bandwidth with the M2P connector. The PCIEX4 slot operates at up to x2 mode when a PCIe SSD is installed in the M2P connector.


1 x M.2 connector (Socket 3, M key, type 2242/2260/2280/22110 SATA and PCIe x4/x2 SSD support) (M2M)
1 x M.2 connector (Socket 3, M key, type 2242/2260/2280/22110 SATA and PCIe x4/x2 SSD support) (M2A)
1 x M.2 connector (Socket 3, M key, type 2242/2260/2280 PCIe x4/x2 SSD support) (M2P)
6 x SATA 6Gb/s connectors
Support for RAID 0, RAID 1, RAID 5, and RAID 10
* Refer to "1-8 Internal Connectors," for the installation notices for the PCIEX4, M.2, and SATA connectors.

It may all just be your cards power saving feature, since in BIOS it says x4 and PCIE 1.0 even! Run the 3D test in GPU-z and see if it goes up

i have:
1 - m.2 (970 evo 250gb)
1 - ssd (ssd 860 evo 500gb)
2- hdd


I tried to disconnect everything and same.. x4...:


Gpu-z test:


btw
Nvidia power m. mode: prefer maximum performance
Windows power options: high performance

Card on another mobo runs fine at x16 (I tried on a friend's computer)

Few things to try. Clear CMOS, then load optimized defaults, and then keep testing for now with single card and single NVME, unless you know by manual the NVME is not affecting. Could possibly be blown resistor or something on the slot?
Does card run at x4 on the x8 slot too, with nothing in the top x16 slot? If yes, then maybe not blown resistor/fuse for the slot. Can you test other card in the top slot, to see if other card is OK and you see x16 there? Maybe some compatibility issue?
If you think maybe it's a compatibility issue after testing you will need to email them and give exact card model, full # of card details, then they can test

1. Method same x4 3.0...
2. On slot 2 (x8) card runs fine at x8 3.0 (with nvme). I will try another card :) on pcie 1 x16 slot.

Update:
I tried old gpu AMD Radeon RX 480 at slot 1. cmos clear+plug in than start but my mobo cant detect this gpu. (at slot 2 works good at 8x)

I tried 1 slot install AMD Radeon RX 480 and another 8x slot gtx 1080 and both work, but 1 slot running at x4 :/.

Probably i need to rma mobo

Yes, sounds like there may be some issue with slot #1 then. Did you try cleaning cards gold finger with alc, and blow out slot to make sure no dust in there causing issue?

yes, the first thing i tried was gpu and mobo gold contacts clean up with alc