Have a look in .gconf/desktop/gnome/interface/%gconf.xml
You're looking for something like:
<entry name="gtk_key_theme" mtime="1194649444" type="string">
Either get rid of the entry block, or change Emacs to Default.
You'll probably have to log out and back in for this to take effect. I'd check the file again once you've done that, as I don't know if/when gconf writes to its config files.