I've had this problem for the longest time but I gave up on it after Asus tech support told me where to shove it. Even if I can't fix it, I'd like to know if anyone else has experienced this and where the actual problem lies. I'm just going to copy and paste most of the problem description.
Motherboard: Asus P8Z77-V
Case: Fractal Design Arc Midi R2
There is something wrong with the internal (Intel) USB 3.0 header when plugging inthe cable from my Fractal Design Arc Midi R2 case. When I plug in a certain USB 2.0 thumb drive through there, it freezes in Windows. When plugging in a different drive (external HDD, USB 2.0), it is able to read from the external hard drive, but writing a (large) file to it fails. Both the AsMedia and Intel USB 3.0 ports at the back panel of the motherboard work fine.
I have tried installing the latest USB 3.0 drivers from both the Asus's support page,as well as the later ones from Intel. Neither fixed the problem. The problem also exists outside of Windows. Although the USB drive will be detected, trying to read from it (i.e. by booting Linux from it) results in read errors.
I used a different USB 3.0 cable (http://www.bitfenix.com/global/en/products/accessories/internal-usb3-adapter), to test it and it worked perfectly, so I thought the problem was the cable. I contacted Fractal Design and got a second USB 3.0 cable from them, but it was the same. Later on, I even got one more cable from them, but the problem still persisted. I had a friend test one of the Fractal Design cables, along with one of my USB drives with his motherboard (also an Asus, but different board) and it worked perfectly for him.
As per Asus's troubleshooting instructions (they claimed it was needed to pass the case to the relevant department), I have tried disabling the Legacy USB 3.0 support int he BIOS. I also removed the board from the case, and connected the USB 3.0 cable from Fractal Design to the onboard USB 3.0 connector on my motherboard. It was a pain to do and the results were still the same. At that point, Asus replied (without ever sending me to the "relevant department"):
"Currently it seems that the usb 3.0 cable of the Fractal Design case have some compatibile issues with some usb 3.0 devices.
So if possible, I suggest you to have a further check with the Fractal for a try."
So really, at this point, I've lost all hope to have a working USB 3.0 port at the front of my case with this setup. I'm just very curious about Asus's claim. Does anyone have the same or very similar setup (i.e. a P8Z77-V variant motherboard and Arc Midi R2 case) and have a working USB 3.0 port through the case's USB cable, plugged into the USB 3.0 header of the mobo?
BTW, I do not have a USB 3.0 device to test it out with. Also, my friend's mobo was an Asus Z9PE-D8 WS.