Install and check to see what GPU-Z say.

GPU-Z reports the Bus Interface as PCIe x4 4.0 @ x4 3.0

The graphics card reports that it supports: PCI-Express x4 4.0

It is currently running at: PCI-Express x4 3.0

I don't think the use of an M.2 drive would decrease the bandwidth allocated to a PCIe x16 slot.  I am guessing that some settings might have adjusted the reading while the RX 6400 is in idle.  If you want, you can check the reading while running load test with FurMark.

Running a FurMark benchmark test did not change anything (AMD Andrenalin & GPU-Z). Thank you for the suggestion and your help.

I have been experimenting with disabling ASPM in the bios and Windows power settings for the balanced power profile (switching PCIE Link state power management to 'off' via the control panel and advanced power options). I did not see any change with reported running speed when on load via FurMark.

I booted into Lubuntu Linux from a USB flash drive. Dmesg reported the following:

31.504 Gb/s available PCIe bandwidth, limited by 8.0 GT/s PCIe x4 link at 0000:00:01.0 (capable of 63.012 Gb/s with 16.0 GT/s PCIe x4 link)

So capable of PCIe Gen 4 speeds.

sudo lspci -vv (in Lubuntu Terminal) gave the following:

LnKSta: Speed 8GT/s (downgraded), Width x4

So the PCIe link status shows 'downgraded' to PCIe Gen 3 speed.

Also just out of curiosity I disabled all onboard storage in the bios and booted Lubuntu via USB and it did not create any difference to the GPU issue.

I also ran the glmark2 GPU benchmark test program in Lubuntu and checked lspci -vv and the was no reported change in speed.

The suggestion to run FurMark was to measure the card performances for comparison.  No change in link speed should be expected.

Part of troubleshooting may suggest to experimenting with different BIOS firmware.

@HarveyJD​

Any update on this OP? I've done the same procedures you've mentioned before I bumped into this thread and sadly, same result. I just wanted to know what possible workaround can we do about this.

Apologies for the late reply. I have not made any changes or experimented since posting about the issue. My RX 6400 is still only using PCIe Gen 3 in the x16 slot.

Are you using the same GPU?

I am thinking to try a different PCIe Gen 4 GPU (Nvidia RTX A400 or Intel Arc A310). They use x8 spec instead of x4 like the RX 6400. This is to eliminate the x4 lane RX 6400 GPU as an issue.

However it is likely that PCIe Gen 4 was never enabled for x16 PCIe slot on the Optiplex 5000 SFF.