Self-Desorgnizing Menu

I have Gnome and KDE in Opensuse 11.4. It seems that the organization of menu items of one WM influences other somewhat but not completely. For example I installed all applications and organized menu in Gnome. Then at the first time I used KDE I switched to classic menu. Gnome menu in 11.4 has fewer entries but KDE had more entries, looking like the way Gnome menu was in 11.3. Then I noticed that some items were not in the same place I left them in Gnome. Example: I placed manually some applications in Gnome menu under Wine entry but in KDE they appear in Applications entry. I tried switching KDE menu to apps launch mode but the categories remain the same.
Having applications in different places is not hard to get used to. But the most puzzling thing is that there are some applications and entries that simply do not appear in kde menu (in both modes). Example: Under multimedia I have an entry “Meida edition” where appears the Audacity icon. In kde neither this entry nor audacity icon appear anywhere at all. But when I try to edit kde menu the entry and the icon are on the list. They just do not appear visibly.
OK. I don’t mind if applications remain in different places from Gnome to KDE. But how can I make sure all applications appear in the menus?