xfree package do not install this file: /usr/X11R6/lib/X11/fonts/encodings/encodings.dir XFree86 project provide it in Xfenc.tgz archive in binary installation. Many things just don't work without it. iso8859-13 characters from Unicode TTF, for example. BTW, it is useless to create fonts.dir in /usr/X11R6/lib/X11/fonts/encodings/ as pkg_postinst() do and adding it to XFS fontpath is not a good idea too.
Check xfree-4.2.1, as its fixed here.
encodings.dir - OK. No fonts.dir in encodings/ - OK. Small glitch to fix - delete encodings/ from /etc/X11/fs/config fontpath (/usr/portage/x11-base/xfree/files/4.2.1/xfs.config).