Tim:
Have you been editing the menus? As well as options for adding or changing menu content, you can simply turn some entries on or off.
Beartooth:
No, I haven't. I know I installed the app to do it, but I'vebeen more concerned with other things, and haven't even tried it.
I just found one, called alacarte.
I thought you were using Fedora 9? You don't need to add an editor program, it should be possible to edit menus just by right-clicking on the top of the menu.
On the machines without the Control Center on the panel, sure enough, it was unchecked there, God knows why. So I checked it, and various other intriguing stuff besides.
I don't know why some computers would be different than others. But the default menus are set up from .desktop files from, at least, within /usr/share/applications/ (though there's other places, too), where you can look through them to see if there's any "hidden" or "OnlyShowIn=Gnome" settings. Hint: locate .desktop
Personalisations are stored inside your homespace, which will override the system ones. Look in: ~/.local/share/applications/
Some .desktop files won't be used directly for menus, they'll be used by other things, that make use of the same format.