after upgrading to Windows 10 Creators Update, one of the several PCI ports remains disabled a device driver in the device manager. It is about:

Intel (R) 5 Series / 3400 Series Chipset Family PCI Express Root Port 3 - 3B46

Also tested clean installation Win 10.
After manual turn it on, the driver work correctly.
I do not see anything in my system problem functionality.
Can you turn it on permanently?