What is in /usr/local/share/applications? That is where those menu items are. Are your menus empty as well? Or even just mostly empty?
I run gnome 2.22. The only other thing I know is that, for gnome2.22 at least, menus are built using files in /usr/local/etc/xdg/menus, like /usr/local/etc/xdg/menus/gnome-applications.menu. Here is someone with that problem.
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