I have tried editing the Main Menu and it doesn't sound like
what you described if I am reading it right. Here is what I
did and see.
Under System I click Preferences and a panel comes up and
on that panel if I right click I have three choices, "Add this
launcher to panel" and "Add this launcher to desktop" and
"Entire menu" and under that menu is, "Add this as drawer
to panel" and "Add this as menu to panel".
If I just left click on "Main menu" I go right into the Main
menu itself. Once in Main menu I can make changes to
what shows up in "Applications and System" and then under
"System" is the two selections for "Preferences and Administration".
Under either I see check marks for what shows up in under
those items on the panel. Bringing up that doesn't have a
way that I can see to add the "Printer" back in to make it a
selectable item under "Administration".