Question about GNOME Desktop

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http://askubuntu.com – OK, so I did a fresh install of Ubuntu 12.04 and completed all updates. I updated to the latest stable kernel. (I think it was 3.5.6, but don't quote me on it) I installed Gnome and the extensions. I did have it working and working well for a few days and then I needed root privileges for a task. As soon as I entered the root command my Gnome desktop went haywire. I rebooted my system and now Gnome looks just like Gnome classic. I can no longer select "shell theme" from "advanced settings". It looks like somehow all of my extensions went away as well. Has anybody ever experienced thi (HowTos)