Version: (using KDE KDE 3.4.0) Installed from: Gentoo Packages The /usr/X11R6 anachronism can be wiped out, since Xorg can be installed as any other FHS conforming application. It won't be nice to get the compatibility symlinks dropped as soon as possible,
An example of a few people having this problem is here: http://forums.gentoo.org/viewtopic.php?t=175229 Temporary solutions are also given there, but as Carsten stated the FHS doesn't require the existence of the symlinks required.
With Xorg modular this is fixed as it installs in /usr/share/X11 and that is checked by kxkb since 3.5.0rc2.
I forgot to mark this bug as closed, I fixed it in revision 487570.