I had what I think was a closely related problem. I am running Gnome Shell in Quantal 12.10 and loaded Nemo to replace Nautilus. Unfortunately, I don't recall how I installed it.
After a while, my desktop failed to render properly. It looked strange; as-if the theme had been lost. The Look-and-Feel of Gnome Shell was gone. The colors made editing filenames on icons impossible. There were a number of other major annoyances.
I followed Andy Braham's advice (from the accepted answer) to remove the software. But then I followed the Noob Labs's blog posting http://www.noobslab.com/2013/10/nemo-file-manager-with-extensions-for.html to reinstall Nemo.
After a reboot, the problem was resolved. I hope it stays resolved. But I'm not sure, since I saw the problem come and go (mostly come and stay) prior to the fix.
[It really seems that Ubuntu is fragmenting into either a) an unacceptably de-featured desktop OS; or b) a difficult to configure desktop OS. Hopefully that will improve eventually.]