Hmm, that's outright annoying. Do you resume from hibernate or from
suspend?

I can only think of 2 other options to try:
- upgrade to a newer kernel (or even try downgrading - see what that does):
http://kernel.ubuntu.com/~kernel-ppa/mainline/

- use software suspend (uswsusp package). Configuring can be a bit
tricky though, as the system suspend/hibernate commands are not
automatically adjusted, so invoke hibernate manually by s2disk .

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https://bugs.launchpad.net/bugs/1413440

Title:
  USB stops working after a while (xhci_hcd 0000:00:14.0: Timeout while
  waiting for setup device command)

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