My motherboard is a Gigabyte Z68XP-UD4 and I bought a 750GB Hitachi Touro Pro. Everything went fine at first with the supplied USB 3.0 cable, I was transferring at 100mb/s but the cable was too short, at 1 foot. I ordered a 6 foot cable from Amazon and once I used that cable, everything seemed to have messed up. Transfers would either freeze or go really, really slow, as in 10mb/s, slower than USB 2.0. The HDD still worked on USB 2.0 ports just fine so I thought it messed up it's 3.0 part.
I thought the cable somehow messed up the HDD, so I exchanged for a brand new one. I am using the supplied cable again, not even touching the cheap cable. Only this time, I am getting different problems. Even with the blue "on" button lit on my HDD, my computer would not read my HDD. It would take a couple jiggles of the cable and it would finally read it, however, it transfers at USB 2.0 speed, maybe a little faster at 40mb/s. Other instances, even with the connection secure, my HDD wouldn't even turn on.
USB 2.0 ports work perfectly fine. This new one doesn't freeze like the one I returned though. I'm thinking the cable might have shorted something out? My motherboard only has 2 USB 3.0 ports and neither of them work. Am I screwed?
If you have to wiggle the cable, either the cable, the port or both are bad. If the motherboard connectors are bad you could add a PCIe USB 3 adapter card. Have you tried re-installing the USB 3 driver -- might even be an updated version?
If you use longer cables use good quality stuff, and while the USB 3 spec doesn't have a specific length limit like the 5 meter limit in USB 2 AFAIK, I would stay below the recommended length of 3 meters.
I have tried re-installing the drivers, but haven't tried updated ones. I doubt this is it as it WAS working prior to getting the cheap cable. I brought my HDD to my friend's place to try and it was indeed my motherboard USB 3.0 ports as it was perfectly fine on his computer at a 100mb/s.