Don't know your full configuration, but that lower M.2 slot shares bandwidth with the PCIE_X8_2 slot, in fact I suspect that both M.2 slots might share that bandwidth. That PCIEX8_2 slot in turn shares bandwidth with the PCIE_X16/X8_1 slot. With a Ryzen cpu:



and with A-Series/Athlon cpu:



Because each M.2 NVME drive requires 4 lanes (PCIE_X4) then with two M.2 drives you are using X8 lanes. So I don't see how you can have two M.2 NVME drives unless you have a single GPU video card and with the PCIE_X8_2 slot unoccupied.
Does that help or is there a different problem?

That makes sense.

I do have single gpu

however i also have an elgato 4k capture card and pci-3 usb card

The USB card is probably X1 and can go into any of the black PCIE_X1 slots under the control of the X370 chipset. Unless you are talking about USB 3.1 maybe with USB C form factor? That would be an X4 USB card then. I am not sure about the capture card. If it uses X4 lanes, you may need to remove the USB card and put the capture card into the black X4 slot? If you put an X4 device there, the three black X1 slots get disabled. You get the idea that these slots share bandwidth so you have to go the manual and plan a strategy. Also it occurred to me that maybe you are setting up the two M.2 for RAID? I am not experienced there, but if you think that is causing the problem, maybe someone can help, who has set up NVME in RAID on the C6E. One way to get more PCIE lanes is to move up to a Threadripper system, but for a lot more dinero!