The problem is USB3 itself. There is a reason why R7000 puts its USB3 in the front.... You can read about it http://www.intel.com/content/www/us/en/io/universal-serial-bus/usb3-frequency-interference-paper.html.
If you're using 2.4 GHz, the slow speed could be due to USB3 interference with the band. You can see the 2.4GHz noise level at System Log > Wireless. If it's high, try wrap your USB3 device with aluminium foil.