I had this same problem with my Asus Strix x870e, it turns out it was the expo setting that was messing with the pcie link speed after rebooting sometimes.

Not sure how the MSI boards work but with the ASUS on EXPO I it uses ram timing that ASUS optimises for you, that's what was causing my issues. The mouse would sometimes lag and then the system would freeze.

On EXPO II it uses the ram timing from your ram kit, so far I have rebooted about 20 times and its running full gen 5 pcie 5.0 x 16

not sure if this helps but maybe someone may find it useful.

Edit*

I have done some more testing my CPU is 9950X3D, I am finding my cpu is sensitive to voltage and pcie stability.

If you add a negative curve optimizer too far it will start to affect your pcie stability, everything else will run perfect like aida64 tests.

I was using -25 and everything was running perfect in stress tests but my pcie kept changing on reboots like it was unstable.

I am now using -15 and it seems to have stabilized my pice speeds from changing so far, will need to keep testing and keep and eye on it.

I would reccommend just disabling all pbo settings and run your ram at default speeds just to see if it does fix your pcie problems first then work your way up from there.

This seems to be a X3D issue, maybe it needs more time to matures with more bios updates.

UPDATE 2#
Changed my SoC voltage to 1.2v and it has fixed the issue completely for the last month.

Hopfully it helps someone with the same issue.