Just checked.

The upstream Kernel versions: 4.1.0-040100rc7-generic #201506080035 and 
3.19.8-031908-generic #201505110938 from 
http://kernel.ubuntu.com/~kernel-ppa/mainline/?C=N;O=D don't seem to exhibit 
this problem.
Will try to do a git bisect between "355957e Linux 3.19.8" and "a52caa6 UBUNTU: 
Ubuntu-3.19.0-20.20" and see what that turns up.

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https://bugs.launchpad.net/bugs/1464723

Title:
  Human interface devices stop working on USB 2.0 ports after some time,
  continue to work on USB 3.0

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