This is a stab in the dark, but since USB 3.0 chipset also uses PCIe, I wonder if you remove all USB devices and access the machine only over SSH are the timeouts less or gone.
I’m only thinking about this because later firmware that the one available for the VF2 fixed some PCIe issues. It is probably a red herring (idiom’s do not translate into all languages, so hence the link). But my thinking is that if you unplug all USB devices there should be no PCIe traffic generated by that lane. At the very least it would cross one item off the list as a possible cause of the problem or shift it much further down the list.