Can you check how your system behaves when you do:

echo 1 | sudo tee /proc/sys/vm/dirty_ratio

I had really slow USB transfer speeds (only to pen drives, not to USB disks), 
and this "fixed" it for me.
(Actually it only cures a symptom, because the default value of 10% dirty cache 
should work just as well.)

Maybe this can help determine the underlying problem.

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https://bugs.launchpad.net/bugs/837070

Title:
  Natty almost freezes on USB transfers / slow transfers / Xorg freeze /
  caching lunacy

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