...seems same problem here

hardware specs: AMD A10-7800, 4x 3.50GHz, Crucial Ballistix Sport DIMM Kit 
16GB, DDR3-1600, CL9-9-9-24 (BLS2CP8G3D1609DS1S00) - Mainboard MSI A88XM-E45 
(7721-004R) Fractal Design Define R4 Black Pearl, silent
be quiet! Straight Power E10 400W ATX 2.4 (E10-400W/BN230), SSD 512 GB 830er 
Samsung

Bug concerns all my USB3 ports, front and rear... sometimes not
detected, sometimes only as USB2 ... in WIN 8.1 all fine.

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https://bugs.launchpad.net/bugs/1242321

Title:
  USB 3.0 Harddrive not recognised

Status in linux package in Ubuntu:
  Confirmed

Bug description:
  Ubuntu is not recognising any device plugged into any USB 3.0 ports.
  Sometimes Ubuntu will freeze for a few seconds when you plug something
  into a USB 3.0 port; when Ubuntu comes out of the freeze, the device
  is still NOT recognised.

  No problems with USB 2.0 ports and devices.

  The USB 3.0 on this computer only works in Windows 7 (I'm dual booting
  Ubuntu 13.10 and Windows 7, both are 64-bit).

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