I've added a QA warning to autotools.eclass so that now using its functions outside of src_unpack throws is reported to the users (and thus to the developers to fix it). I'm filing bugs for the packages I can easily find being doing this through a simple grep on the tree. If you fixed the issue in the last version of an ebuild and I still opened this bug, please don't close it until you removed that ebuild from the tree. Thanks for the cooperation.
Fixed, http://overlays.gentoo.org/svn/proj/webapps/migration/sci-geosciences/mapserver/ Will be InCVS as -r1 shortly.
mapserver-5.0.0-r1 in cvs.