Hi cheater1034,
The kde menu uses the freedesktop specification.
The hard answer is that you should have a look at the spec and see how it works.
http://standards.freedesktop.org/menu-spec/latest/
I was quite surprised, but I solved some menu problems.
I can't say too much because I only know how it works in Suse. The KDE site will tell you how it works in your distro.
In Suse, when you change the menu, a local file in your home dir contains the changes. In Suse it is
/home/username/.config/menus/applications-kmenuedit.menu
Problems with the menu editor are quite common.
When you look at that file and the spec you will see why: the local/user file is full of details about items that are tagged with "moved", "deleted", "not deleted" -- it is not the actual menu but more like like a record of what you did with the menu editor.
As a general rule, with the editor, I find it best to make only a few changes at a time and then save and see how it looks.
I'm a bit pressed for time, but hope his helps.