I have had a similar problem. While working in gksudo nautilus, all my
icons became generic & the desktop became non-responsive. Upon reboot I
was not able to login to my user--I have enabled root on my system &
allowed admin logon--that was the only way I could get in my system. I
found in my case that /tmp had permissions changed in a way that my user
could not write to it--I changed permissions on /tmp & could use again.

I think that nautilus is changing permissions at various places in the
system whilst using root.

-- 
 copy as root  trashes my install
https://bugs.launchpad.net/bugs/250021
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