I had this issue after the September 11, 2018 update.
- Device manager showed only my 3.0 ports installed but they were not working and no yellow exclamation marks.
- I right clicked on the USB controllers item and had to enable it. No Change
- Then I right clicked on the intel 3.0 eXtensible item and clicked update driver. "Latest driver is installed"
- Then I right clicked on the USB 3.0 item and enabled that and all my drivers came back.
Hope this helps.