I have the same problem with my Life-book notebook.
Some times the USB 3.0 ports will run in USB 2.1 Protocol and some times they will run in USB 3.0 protocol
I am trying very hard to figure out what is the reason behind this. I have 3 USB 3.0 ports and 2 of them will run in 2.1 protocol and one will work in 3.0 protocol but the usb mass storage will always show up in the xHCI controller on on my USBVIEW.exe program.
The xHCI controller is the USB 3.0 controller. You can see what devices run on the controller in USBVIEW.exe to make sure they are running on the correct USB 3.0 controller.
The problem is, they are running at USB 2.1 protocol and not USB 3.0 protocol.
If I change operating systems, the same problem happens. This is very odd. I wish I knew what was causing my USB 3.0 port to run these USB 3.0 devices as USB 2.1 protocol and not USB 3.0 protocol.
By the way I am running INTEL 7 series C216 chip-set USB controllers and intel xHCI controllers.
I use chipgenius to see the USB protocol version when the USB 3.0 is running slow and I use USBVIEW to see what controller the USB mass storage is working with.
The USB 3.0 ports seem to change quite often what protocol they run my USB 3.0 USB drives at. Sometimes they all run protocol 2.1 and its slow. Some some of them run 2.1 and some run 3.0. Sometime they all work.
I wish I could get them to run USB 3.0 protocol all the time.
The controller seems to be switching between 2.1 and 3.0 and I have no idea why or how to control it.