I have the exact same problem, I bought a NZXT Switch 810 case, it comes with Front Panel 2x 3.0 USB slots, one of them does not work. I have built in USB 3.0 on back panel... and the Front Panels come with a blue connector but like I said only one out of two work.
NZXT Switch 810 Case
MSI Z77A GD80 Mobo
Anything else does not seem relevant for this issue! I truly hope its not faulty hardware, is there a possible driver/software issue here?