I'm sorry for the late response. This problem only happens when I use my 
docking at work, but I usually only have time for playing around at home, where 
there's no docking.
Unfortunately the bug also exists in the mainline kernel.

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

** Tags added: kernel-bug-exists-upstream

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

Status in linux package in Ubuntu:

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
  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
   /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 
  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
   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.product.name: Latitude E7440
  dmi.product.version: 01
  dmi.sys.vendor: Dell Inc.

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