I am having this exact problem. It works for a few minutes, then cuts out?
I suspect that my problems are actually due to my physical ports on the case (Corsair 400R.) There have been a number of complaints about this particular case. I have a replacement panel on order and we'll see if that takes care of the issue. If it doesn't, I'll likely have to RMA the motherboard back to ASUS.
FWIW, my ports work sometimes for a long time and then other times, will not work at all (mostly the later.)