Based upon the original discussion, to the best of my knowledge, this issue still has not been corrected. I am waiting for Apple to fix the USB 3.0 issue, but so far, no luck.
I have a friend who bought a 15" rMBP when it first came out. He has been in negotiations with Apple nearly ever since regarding USB 3.0. So, he has owned (and returned most) 14 USB 3.0 hubs, none have worked well. He owns 5 USB 3.0 drives, maybe more. We have gone through many troubleshooting steps, and found that some hubs worked better than others, and some drives better than others, but nothing was consistant. He has Win7 on Bootcamp partition, so I had him try that, same thing, inconsistant results.
We had another friend with a Win7 PC portable try what we had been doing with the rMBP, the PC worked flawlessly. Well, there was one minor thing, but I'm pretty sure it was a user error, not the machine's fault, and it was very minor as compared to the sometimes not recognizing drives on the rMBP.
So, this points to most likely the SMC firmware on the rMBP, at date of writing this 2.3f32, and boot ROM is MBP101.00EE.B03 (it's .B02 on my friends rMBP), I checked these facts with the very latest that Apple has released at the Apple Store. It's unlikely the boot ROM will have an impact of the functioning of USB ports, more likely the SMC which controls nearly all interfaces.
It is possible, but less likely that Apple has bad drivers in both Mac OS X 10.x for USB 3.0, and bad drivers for bootcamp. So I'd stick with the SMC firmware to be the most likely culprit.
If anyone hears about a firmware update for rMBP, could you please post it on this thread? I will keep watching for the same.🙂