I want to update the thread; my computer clicked again (with a strange
beep noise) while shutting down. I am still using Debian Wheezy Xfce,
with gvfs removed. Thus, I can confirm that gvfs is not the real cause
of the problem.
The only applications open were VLC and my web browser. I am not sure if
they had anything to do with this noise and click problems anyway.
I am considering to change my hd soon; but I may also install another
distro like opensuse or fedora instead of a debian based one (although I
would like to stay with debian). I haven't made up my mind yet.
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