So your Phantom has the updated USB 3.0 input on the case? Older ones (like mine) do not have a USB 3.0 input on the case, although you can get a new I/O panel. The cases I/O panel has the USB3.0 cable connected to the USB3.0 connector on your board of course?
Not sure what UEFI version you have, could be 1.60 after your update, which has a USB compatibility update.
There are drivers for the Intel and Etron chip USB3.0 support on the board, and IME and the chipset (inf) files must be installed, just to review. Your boards back panel has four USB3.0 ports from the Etron chips, and two from the Intel Z77. I would try the back panel USB3.0 ports with a USB3.0 flash drive for testing. If you can ID which ports are which, that might help narrow things down.
My Z77 EX4 board has no problems with the USB3.0 inputs. The USB3.0 inputs on PC cases can be flaky, I had to have them replaced on a Corsair case.