1. update to the latest menudrake and menu rpms from apt-get
2. delete everything in the /etc/menu directory
3. delete the applnk-mdk and applnk-mdk-simplified directory in .kde/share
4. delete the .menu directory in home
5. update-menus -v when it stops press return to get to the konsole prompt
6. run menudrake and save
7. check your kcontrol to make sure everything is still there.

Now you should be able to edit your menus as needed and not lose kcontrol settings.