I am having the same problem, for some reason I cannot get my HBA, Raid Controller, or NVME to run at PCIE3 speed, I tried running vmware with passtrough or windows os on baremetalHmm, for some reason I remember that to get PCIE 3 on my SM Board I would need to upgrade to a V2 chip.
Looking at intel ark site E5-2620 v1 have PCIe Revision 3PCI-e bus from the cpu..so forget about it