I'm running the X99-UD4 and I'm not having any problems with USB or anything with hard drives. I'm running win 7 on array and windows 10 on a M2 SSD. I have 2-240gb SSD, 4-600gb WD raptors, DVD, & DVD/rw.
The only problem I'm having is a BSOD once in awhile. I have been running this board from almost the day it came out. Plus I would still be on the bios that it came with. But I tried a newer bios to see if it would fix the BSOD NO.
I have sitting in the backroom for sale from a review a EVGA X99 Classified, ASUS X99-E WS, & ASUS X99-A. I could try one of them but I really happy with the Gigabyte board.
I don't run windows 8.1 because of all the problems with it. Yes I know windows 10 is windows 8 with all the fixes. But it is just a test OS. On the BSOD I'm not worry about it. I don't worry about the small stuff.
One other thing is I have been doing this for over 30 yrs. When is comes to motherboards it really is a flip of the coin which one you use. They all have their problem. I've used mostly Abit, Soyo & now Gigabyte.