I have this same motherboard and the USB 3.0 ports are not working. Did your replacement motherboard fix your issue?
Here is the semi-short version of the story.
I contacted Amazon again and let them know this was a known issue. I provided evidence of this using the feedback from Gigabyte support, and various other forums.
Amazon, being none too happy with this, pulled the item temporarily from the website while they investigate the issue. After a few days, it went back up for sale, but I could not get a straight answer whether the motherboards were REV 2, or the older REV 1 versions.
At first I opted to exchange these defective motherboards with an ASUS brand, but because of my requirements I ended up taking a chance and changing my order to the TH (Thunderbolt) model instead, hoping that it would have the REV 2. It did, and so since then I have not had any issues with the motherboard.
Now, before we assume everything is ok. I have not turned off, or unplugged this PC since I first booted it up. That is usually when the USB ports failed because from what I can gather, it seems that unplugging the power puts the USB ports into a "stuck" state indefinitely. I'm sure sure that is true, but I can't call this "fixed" until I attempt this.
So, in the end, if it weren't for the fact that I am building a Hackintosh, and there is a lack of support for the ASUS motherboards, I would have dropped Gigabyte for good.
Lets just hope that this revision has fixed the issue. My advice is to go with another brand if possible. If you're stuck with Gigabyte, then contact them and request and advanced RMA replacement. You'll have to pay to ship your defective board back (which I think is ridiculous), but at least the chances of it working will be better.