Comment 5 for bug 344343

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.