The problem seems to have gone away. I don't know when it was fixed for me, has 
there been a recent kernel update?
After reporting this bug I reinstalled using kubuntu installer, but later 
switched to mate desktop. I do know the problem was still present after 
installing kubuntu, but it has gone away some time after that.

** Changed in: linux (Ubuntu)
       Status: Confirmed => Fix Released

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https://bugs.launchpad.net/bugs/1626870

Title:
  USB-devices connected to dockin not recognized when connected at boot

Status in linux package in Ubuntu:
  Fix Released

Bug description:
  My laptop is mostly connected to a docking station in my office. If
  the computer is docked when booting, the USB devices (keyboard, mouse)
  are not detected. If I remove the computer from docking and then
  reinsert everything works as expected. Monitors and network connected
  to the dock does not have this issue.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: linux-generic 4.4.0.9136.37
  ProcVersionSignature: Ubuntu 4.4.0-9136.55-generic 4.4.16
  Uname: Linux 4.4.0-9136-generic x86_64
  ApportVersion: 2.20.3-0ubuntu7
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC2:  andreas    5094 F.... pulseaudio
   /dev/snd/controlC0:  andreas    5094 F.... pulseaudio
   /dev/snd/controlC1:  andreas    5094 F.... pulseaudio
  CurrentDesktop: Unity
  Date: Fri Sep 23 09:22:41 2016
  HibernationDevice: RESUME=UUID=a573b0e2-8ed1-4d22-9313-8e552c603b2f
  InstallationDate: Installed on 2016-07-13 (71 days ago)
  InstallationMedia: Ubuntu 16.04 LTS "Xenial Xerus" - Release amd64 
(20160420.1)
  MachineType: Dell Inc. Latitude E7440
  ProcFB: 0 inteldrmfb
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.4.0-9136-generic 
root=UUID=cdbcc31e-7f7d-4ad9-b46d-5299d8f494ec ro quiet splash vt.handoff=7
  RelatedPackageVersions:
   linux-restricted-modules-4.4.0-9136-generic N/A
   linux-backports-modules-4.4.0-9136-generic  N/A
   linux-firmware                              1.161
  SourcePackage: linux
  UpgradeStatus: Upgraded to yakkety on 2016-09-20 (2 days ago)
  dmi.bios.date: 05/19/2015
  dmi.bios.vendor: Dell Inc.
  dmi.bios.version: A15
  dmi.board.name: 0JNYGR
  dmi.board.vendor: Dell Inc.
  dmi.board.version: A00
  dmi.chassis.type: 9
  dmi.chassis.vendor: Dell Inc.
  dmi.modalias: 
dmi:bvnDellInc.:bvrA15:bd05/19/2015:svnDellInc.:pnLatitudeE7440:pvr01:rvnDellInc.:rn0JNYGR:rvrA00:cvnDellInc.:ct9:cvr:
  dmi.product.name: Latitude E7440
  dmi.product.version: 01
  dmi.sys.vendor: Dell Inc.

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