I also had this problem, and found a different fix in 4.9 that fixed it
(my original bug #1641052):

commit a8006bd915095c40098bfcb684cc2bdfb414dc0d
Merge: 965c4b7 6bad6bc
Author: Linus Torvalds <torva...@linux-foundation.org>
Date: Fri Oct 28 11:26:01 2016 -0700

    Merge branch 'timers-urgent-for-linus' of
git://git.kernel.org/pub/scm/linux/kernel/git/tip/tip

    Pull timer fixes from Ingo Molnar:
     "Fix four timer locking races: two were noticed by Linus while
      reviewing the code while chasing for a corruption bug, and two
      from fixing spurious USB timeouts"

    * 'timers-urgent-for-linus' of 
git://git.kernel.org/pub/scm/linux/kernel/git/tip/tip:
      timers: Prevent base clock corruption when forwarding
      timers: Prevent base clock rewind when forwarding clock
      timers: Lock base for same bucket optimization
      timers: Plug locking race vs. timer migration
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https://bugs.launchpad.net/bugs/1630063

Title:
  specific USB devices disconnect and don't reconnect

Status in linux package in Ubuntu:
  In Progress
Status in linux source package in Yakkety:
  In Progress

Bug description:
  2 USB ports randomly disconnect and don't reconnect (it's always the
  same two), and in dmesg all I get is

  "
  [ 1276.916458] ohci-pci 0000:00:12.0: HcDoneHead not written back; disabled
  [ 1276.916467] ohci-pci 0000:00:12.0: HC died; cleaning up
  [ 1276.916553] usb 3-1: USB disconnect, device number 2
  [ 1277.017302] usb 3-2: USB disconnect, device number 3
  "
  This only started happening when Yakkety went to the 4.8 branch, with 4.7 
branch this doesn't occur, hence the bug report since it's unlikely that a 
hardware failure will only stick to one OS and one branch of the kernel for 
that OS. (these USB ports don't randomly die on Windows or BSD, I've tested 
that in the past couple of days)

  
  kernel version: 4.8.0.17.27
  Ubuntu version
  Description:  Ubuntu Yakkety Yak (development branch)
  Release:      16.10
  --- 
  ApportVersion: 2.20.3-0ubuntu7
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC1:  c_smith    2213 F.... pulseaudio
   /dev/snd/controlC0:  c_smith    2213 F.... pulseaudio
  CurrentDesktop: MATE
  DistroRelease: Ubuntu 16.10
  HibernationDevice: RESUME=UUID=1a29baaa-55ea-4817-ba45-8c618f65ec4b
  InstallationDate: Installed on 2016-10-03 (0 days ago)
  InstallationMedia: Ubuntu-MATE 16.10 "Yakkety Yak" - Alpha amd64 (20161002)
  MachineType: Gigabyte Technology Co., Ltd. GA-78LMT-S2
  NonfreeKernelModules: nvidia_uvm nvidia_drm nvidia_modeset nvidia
  Package: linux (not installed)
  ProcFB: 0 VESA VGA
  ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-4.8.0-17-generic 
root=/dev/mapper/Linux-root ro nomodeset quiet splash vt.handoff=7
  ProcVersionSignature: Ubuntu 4.8.0-17.19-generic 4.8.0-rc7
  RelatedPackageVersions:
   linux-restricted-modules-4.8.0-17-generic N/A
   linux-backports-modules-4.8.0-17-generic  N/A
   linux-firmware                            1.161
  RfKill:
   0: phy0: Wireless LAN
        Soft blocked: no
        Hard blocked: no
  Tags:  yakkety
  Uname: Linux 4.8.0-17-generic x86_64
  UpgradeStatus: No upgrade log present (probably fresh install)
  UserGroups: adm cdrom dip lpadmin plugdev sambashare sudo
  _MarkForUpload: True
  dmi.bios.date: 01/09/2014
  dmi.bios.vendor: Award Software International, Inc.
  dmi.bios.version: F6
  dmi.board.name: GA-78LMT-S2
  dmi.board.vendor: Gigabyte Technology Co., Ltd.
  dmi.chassis.type: 3
  dmi.chassis.vendor: Gigabyte Technology Co., Ltd.
  dmi.modalias: 
dmi:bvnAwardSoftwareInternational,Inc.:bvrF6:bd01/09/2014:svnGigabyteTechnologyCo.,Ltd.:pnGA-78LMT-S2:pvr:rvnGigabyteTechnologyCo.,Ltd.:rnGA-78LMT-S2:rvr:cvnGigabyteTechnologyCo.,Ltd.:ct3:cvr:
  dmi.product.name: GA-78LMT-S2
  dmi.sys.vendor: Gigabyte Technology Co., Ltd.

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