This bug is missing log files that will aid in diagnosing the problem.
>From a terminal window please run:

apport-collect 1649039

and then change the status of the bug to 'Confirmed'.

If, due to the nature of the issue you have encountered, you are unable
to run this command, please add a comment stating that fact and change
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This change has been made by an automated script, maintained by the
Ubuntu Kernel Team.

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

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https://bugs.launchpad.net/bugs/1649039

Title:
  USB 3.1 controller does weird magic: appears after Windows 10,
  disappears otherwise

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  I have motherboard GA-Z170X-UD5 TH with 2 USB Type-C (USB
  3.1/Thunderbolt 3) ports, BIOS version F20b.

  Both ports are "sleeping" on cold start - I can't boot from USB device
  plugged into any and both of these 2 USB Type-C ports. Ubuntu 17.04 as
  of December 11 doesn't see anything (no messages in dmesg).

  But magically situation changes when involve Windows 10 to the party.
  I boot into Windows PE based on Windows 10 and it happily see flash
  drive and my Nexus 6P connected to both ports.

  After this without unplugging mentioned devices I reboot into Ubuntu
  and "magic" - both flash drive and Nexus 6P work fine through these 2
  USB Type-C ports. Even though it works in Ubuntu, BIOS still doesn't
  see anything.

  nazar-pc  ~  lspci -d ::0c03 -k                                             
                                                                                
                                                                           
  00:14.0 USB controller: Intel Corporation Sunrise Point-H USB 3.0 xHCI 
Controller (rev 31)
        Subsystem: Gigabyte Technology Co., Ltd Sunrise Point-H USB 3.0 xHCI 
Controller
        Kernel driver in use: xhci_hcd
  0b:00.0 USB controller: Intel Corporation DSL6540 USB 3.1 Controller [Alpine 
Ridge]
        Subsystem: Device 2222:1111
        Kernel driver in use: xhci_hcd

  But things are even more interesting: when I unplug either Nexus 6P or
  flash drive and then plug back - they still work fine! But as soon as
  I unplug both of them - Ubuntu doesn't see anything and doesn't post
  anything into dmesg until I boot into Windows 10 again. Interestingly,
  USB 3.1 controller disappears:

  nazar-pc  ~  lspci -d ::0c03 -k                                             
                                                                                
                                                                           
  00:14.0 USB controller: Intel Corporation Sunrise Point-H USB 3.0 xHCI 
Controller (rev 31)
        Subsystem: Gigabyte Technology Co., Ltd Sunrise Point-H USB 3.0 xHCI 
Controller
        Kernel driver in use: xhci_hcd

  nazar-pc  ~   cat /proc/version_signature                                   
                                                                                
                                                                           
  Ubuntu 4.9.0-10.11-lowlatency 4.9.0-rc8

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