Same issue here. Xubuntu, Latest LTS release: 14.04, Trusty Tahr
I am using an external DVB USB device which suffers from data loss using the linux xhci driver when streaming on my DN2820 NUC. Using two cards on the same hub even causes the usb stack to crash completely.
A workaround is to disable the first (front) USB port. This forces linux to use the ehci driver which works just fine with the backside USB 2.0 ports.
But of course this is no satisfying option. While the bug itself might not be intels fault (though I wouldn't bet on that yet even though linux is known for USB 3.0 issues ;-) )
PLEASE RE-ADD the Bios option to disable XHCI in the bios! (Why did you remove it anyway? The more options in the bios, the better...)
Thanks
p.s. an option to disable USB power in S3 sleep mode (not only S5) would also be highly appreciated...