I've had lots of USB 3.0 trouble. When it works, it's great, but 3 different PCIe USB 3.0 cards on other systems I have work not at all or intermittently. USB 3.0 on my old P55A-UD4P always works. On my UD5H, the F_USB30_2 & F_USB30_3 headers both work fine with the GB front bracket and with my front case ports. The F_USB30_1 header has been flaky (Corsair flash voyager GT is not recognized on first insertion after boot but then works fine after that - all under Windows 8 with its built-in USB 3.0 drivers). So I learned that when a device doesn't work in a USB 3.0 port, that doesn't necessarily mean it won't work the next time I plug it into thew same port.
If I understand, your bracket is plugged into F_USB30_2, then the two front USB ports are cabled into the two ports on the bracket. When you switch the two front case port cables, it is always the same front port that is not working, but the other always works? In that case (no pun intended), I would assume that the problem is in the front case port or its cable. I would also check by plugging the USB 3.0 device directly into each of the two ports on the GB bracket to make sure the problem lies after the GB bracket, and so also after the MB header.
I bought a rear USB 3.0 bracket for $8 (free shipping):
It works fine and the price is right. It gave me more ports to switch around when troubleshooting to rule out parts of the hardware. My external USB 3.0 backup drive is on one of my rear ports, all of which have always worked fine.