Make sure you have also enabled the PCIE mode inside the M2_1 Configuration menu. What else comes to mind is changing the settings PCIe speed within the PCI Express Configuration menu. Let us know what's going on.
I am fairly certain I have done that. I am wondering if it is because I have a card at PCIex 1_1? I cannot find anything in the manual indicating that would affect it. I will report back on the bios settings. To clarify, M2_1 is working fine at x4 mode. The issue is M2_2 seems to only report x2, even with manual setting x4 in BIOS. Again I will double check bios settings.
So I've been trying to figure this out but I think you will have to test your PC's without any PCIE_X slots. Try just leaving your graphics unit and testing with the M2 slots installed, then adding each PCIE_X component one by one (if you have any) and testing the computer to see the speeds of the M_2 slots.