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Looking around, it seems more and more like it might be that the CPU might be faulty. First time in 25 years of computing that I've come across a faulty CPU. That's why I'm hoping it's either a motherboard issue, but it can't be, seeing as the system should be running fine with all stock settings.
 

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How do the NVMe talk to the cpu? On the b550 they use the PCIe normally allocated to the gpu. Putting 2 or more NVMe drops the gpu to x8. On the unify/ace only the first slot talks directly to cpu. The other two talk to the chipset.
 

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On the X570 Tomahawk, M2_1slot connects to the AMD CPU and the. M2_2slot connects to the X570 chipset. Neither seem to affect PCI_E1 modes.

Using integrated Vega or Radeon graphics on the AMD CPU drops PCI_E1 to PCIe 3.0 x8.
 
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