I had a great deal of trouble finding a solution to this bug (which was closed without resolution):
Having trouble with my custom launchers not displaying on the "Applications" menu, but they are present when viewed from applications:///
I don't remember which packages caused this because I updated multiple times before I had a chance to reboot. My custom launchers disappeared from the "Applications" menu the last time I logged in.
I've reverted to default menu (rm -R ~/.gnome2/vfolders), and tried adding new launchers, still no go.
You can fix this problem be deleting any empty keys in the files located in ~/.gnome2/vfolders/applications as described here:
Since gnome 2.10 is firing to go, something like applications:/// will be depreciated(no longer supported) by new gnome-vfs version, new gnome-menus will take part of this place and support f.d.o standards, in other words, to make a new menus entry, just put one correct desktop file into /usr/share/application or under your home folder, so the bug you mentioned is reasonably closed.