Some further infos.
I noticed that this happens expecially after I used the same hard drive with 
another computer, a notebook with Windows XP, while after being attached to 
another desktop computer (again with Windows XP). Could it be related to some 
energy saving issue? 
Maybe the notebook sets the hard drive to shutdown after some minutes, but 
Ubuntu cannot handle this setting.
Is there any way to check energy saving settings on usb drives?

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USB Hard Drive randomly unmounted and mounted again
https://bugs.launchpad.net/bugs/178124
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