I ran into this problem.  I installed some Shiki-Colors themes, but
hadn't installed the corresponding icon theme ahead of time.  So I
deleted those themes using the delete button in Appearances, installed
the right icon themes and then tried re-installing the shiki themes.
The same directory over directory error occurred.  Using this thread
http://ubuntuforums.org/showthread.php?t=1040277, I was able to correct
the error.  It seems the delete function from appearances doesn't delete
the folders in your .themes folder in the home directory.  Once you
manually remove these folders, you can install the original theme again.
A new theme was able to be installed correctly throughout this process
for me.

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Installation for theme "name_of_the_theme" failed. Can't move directory over 
directory
https://bugs.launchpad.net/bugs/344343
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