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.
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
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.