I believe I have fixed mine. Perhaps someone else can test the fix on theirs?
>From this 
>http://unix.stackexchange.com/questions/91027/how-to-disable-usb-autosuspend-on-kernel-3-7-10-or-above

Edit the /etc/default/grub file and append to the GRUB_CMDLINE_LINUX_DEFAULT 
line:
usbcore.autosuspend=-1

sudo update-grub
reboot

I don't appear to be getting the disconnects anymore.

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https://bugs.launchpad.net/bugs/1371233

Title:
  USB 3.0 connection is unreliable + xHCI xhci_drop_endpoint called with
  disabled ep

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