I see it has 1 pci-e 5.0 x16 slot, 1 pci-e 4.0 x 4 slot, 1 pci-e 4.0 x4 slot. The SATA ports are 3 pci-e 5.0 m.2 and 1 pci-e 4.0 m.2
Not sure why it would be 1x? I assume you are not running RAID and is set to AHCI? I agree with @jake99 that the kernel parameter may be the answer.