When right clicking on the Gnome foot menu, and selecting edit menus, the system goes off and checks all the menus - then promptly doesn't display all the items. An example of this is LinuxConf, off the system menu, which consistently fails to be found. I am running this as root - and yes, I went into Gnome as root specifically to run LinuxConf, as I know you can't see it as a user... :)
Some of the menu items come from /etc/X11/applnk, which gmenu doesn't know how to edit.
The menu mess is totally redone for GNOME 2, deferring until then.