I saw your post and am looking further into the issue. may take a bit of time to do so
A couple questions
Is this the first reboot since the problem was fixed? (i'm wondering if a pattern where it's fixed after install/reboot and always broken again after the next reboot)
When USB 3 not working, open DevMgr. In the menu bar click View->Devices by connection. Now click to expand the ACPI devices, till you see PCI bus. Expand PCI too. Find your USB 3.0 controller. Note everything is show in parent/child relationship. Make sure to expand all the children so i can see what, if any, devices are connected to your USB 3 controller.
The give me a screen. My example below is of a USB 2 controller as I don't have USB 3.0.. I outlined and expanded all the devices connecting to my USB 2 controller
If you hate the native Windows 8 interface (like i do) install Classic Shell. You can switch back and forth between Windows 7 style menus and Desktop look vs. Windows 8 metro with a mouse click