I've tried using the OC and Normal GPU BIOS, also tried flashing the Normal BIOS with the latest version (was the latest already, but just in case) and the issue persists.
I've updated the MB BIOS to 2.10 and that didn't fix it.
I have only 2 NVME PCI 4.0 SSD in the M.2_1 and M.2_2 slots installed.
The GPU in the PE1 slot shows 4x Gen4 in BIOS using the Auto option. I've tried changing it to Gen4 but that didn't fix the issue.
 
I'll request a RMA for the GPU because of the lanes issue. Also I'll request a RMA for the MB because it doesn't work properly with my old GPU and the PC turns off instead of going to sleep.