Kile bug 314580: A customized toolbar makes settings entries disappear in menu
Looking at a working kileui.rc shows:
After changing a toolbar, this entry has changed to
<Menu noMerge="1" name="settings">
and some entries disappear. If you remove the added 'noMerge'-Tag, all entries in the settings menu appear again.
So I think that a commit, which was added in KDE 4.9.2, is responsible for this:
Commit: Set noMerge=1 for menus when saving the xml file in kedittoolbar
But I have no idea to solve this.