Thank you for providing the test kernel. I am afraid this does not
resolve the issue.

As mentioned in the upstream bug report, it turned out that the problem
is triggered in the xhci-pci code and caused by an ExpressCard Renesas
uPD720202 USB 3.0 controller. I was able to narrowed the issue down to
commit 0e1f0ea which forces a PCI reset on that device at startup and
have reported the problem to the linux usb mailing list:

https://marc.info/?t=150565318600001&r=1&w=2

It looks like the reset leaves the controller in an unstable state, triggering 
 - pipe A vblank wait timed out and
 - pipe B vblank wait timed out
kernel messages.

On my machine reverting the mentioned commit reliably resolves the issue
for kernel versions 4.12.8, 4.13.1 and 4.13.2. The same is true for
removing the external ExpressCard.

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https://bugs.launchpad.net/bugs/1716747

Title:
  linux 4.12 - high system load and mouse delays - pipe A vblank wait
  timed out

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