(applies to Kate/KDE 4.1.2, but only 4.0 is available in the version list.) Thanks to XMLGUI and the KPart system, there are two "Bookmarks" menus when you open any text file in an embedded KatePart with Konqueror. No idea about a possible solution, but I guess it's a usability issue nonetheless.
*** This bug has been marked as a duplicate of bug 158128 ***