It seems like the problem could be Windows* not recognizing the ports correctly.
Please follow these steps in the same order:
Uninstall the USB 3.0 drivers from programs and features then go under Device Manager to uninstall the USB 3.0 drivers.
Restart the computer and reinstall the latest USB 3.0 driver from the Intel(R) web site.
If the problem continues, the operating system may be corrupted, make sure that this operating system installation was performed with this same configuration and not in an older system.
I tried your suggestions, unfortunately no luck on resolving the issue with a driver re-install. I will try a clean install as soon as I can drag my user away. Will let you know how it goes...