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

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Hi,

I have motherboard GA-Z170X-UD5 TH with 2 USB Type-C (USB 3.1 Gen 2/Thunderbolt 3) ports, BIOS version F20b (latest as of today).

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, Linux kernel 4.9 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 Linux with kernel 4.9 and "magic" - both flash drive and Nexus 6P work fine through these 2 USB Type-C ports. Even though it works in Linux, BIOS (UEFI) still doesn't see anything, can't boot from them.

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. However as soon as I unplug both of them - Linux doesn't see anything and doesn't post anything into dmesg until I boot into Windows 10 again. Interestingly, USB 3.1 controller also disappears:

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

Power is always delivered to both ports, fast charging for Nexus 6P works fine.

cat /proc/version                                                                                                                                                                                                       
Linux version 4.9.0-040900-lowlatency (kernel@tangerine) (gcc version 6.2.0 20161005 (Ubuntu 6.2.0-5ubuntu12) ) #201612111631 SMP PREEMPT Sun Dec 11 21:39:11 UTC 2016


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