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.
Only applies to version 1.0.10. Will remove that one soon...
1.0.10 is gone now.