Hi, the installation of kde 3rd-party applications to /usr instead of $KDEDIR is a stupid idea, it breaks almost every 3rd-party app's behaviour. The whole kde environment was never meant to be installed directly to /usr, but into a separate directory (which also is a major pain in the arse); hence the strange directory structure under $KDEDIR/share. You could make the world very happy "un"fixing this issue by emerging all kde related packages to $KDEDIR. This would generally be a good idea, as KDE itself doesn't know anything about the "gentoo way" of setting $KDEDIRS, but normally (and so do almost all 3rd-party apps) uses $KDEDIR. Please be so kind and stop this madness; besides the aforementioned issues breaking other apps, you found a nice way to pollute the file system by emerging things which belong together to different places: no one wants (or needs) two separate $KDEDIR/share/{applnk,apps,...} directories.
The reason for this behaviour is to make 3rd party kde apps work in every KDE installed when there's more than one (e.g. stable+current cvs). Using KDEDIRS for that purpose is officially supported by kde and that's what the KDEDIRS variable is for in the first place (it is not a Gentoo invention, it is a functionality of kde itself). Please report any _specific_ issue you have with this approach and I will try to help you. Noone but you has a problem with approach itself in general that I know of, and it has proven to work very nicely.