It's seems as if this may be a dead article, but hopefully
bmschkerke will be able to benefit from it anyway.
I, too, ran into the same problem. I had three instances of Kaffeiene in my menu and just didn't want them in there. Ran KMenuEdit and got the duplicates. I figured that there had to be something in the settings that was making it so.
Here's what I found to remove my duplicate entries.
browsed to '/home/<username>/.config/menus'
opened 'applications-kmenuedit.menu' in my favorite text editor for KDE.
In there I saw this bit of information.
Code:
<Menu>
<Name>Multimedia</Name>
<Menu>
<Name>Music</Name>
<Layout/>
<Exclude>
<Filename>kde-kaffeine.desktop</Filename>
</Exclude>
</Menu>
<Menu>
<Name>Jack and More</Name>
<Deleted/>
</Menu>
<Layout>
<Merge type="menus" />
<Menuname>Administration</Menuname>
<Separator/>
<Menuname>AudioPlayer</Menuname>
<Menuname>Burning</Menuname>
<Menuname>CD Tools</Menuname>
<Menuname>CD</Menuname>
<Separator/>
<Menuname>Jukebox</Menuname>
<Menuname>AudioVideoEditing</Menuname>
<Menuname>More Programs</Menuname>
<Menuname>Music</Menuname>
<Menuname>AudioVideoRecorder</Menuname>
<Menuname>Sequencer</Menuname>
<Menuname>TV</Menuname>
<Menuname>VideoPlayer</Menuname>
<Menuname>Mixer</Menuname>
<Merge type="files" />
<Filename>realplayer.desktop</Filename>
</Layout>
<Menu>
<Name>CD</Name>
<Layout>
<Merge type="files" />
<Filename>kde-kscd.desktop</Filename>
</Layout>
</Menu>
<Menu>
<Name>Jukebox</Name>
<Layout/>
</Menu>
</Menu>
<Menu>
<Name>.hidden</Name>
<Include>
<Filename>kde-kaffeine.desktop</Filename>
</Include>
</Menu>
The Section in Red, I removed and then saved the file. Clicked on the menu, and viola, duplicates gone.
Hope this helps.