When using my test layer against oe-core (http://gate.crashing.org/~fray/meta-test.tar.gz), the system is unable to detect duplicate functions unless I set the parsing threads (BB_NUMBER_PARSE_THREADS) to 1.
See comments to 4459, there are several issues here, all separate but interlinked.
Patches on bitbake mailing list to resolve this.
Fixed in master with http://git.yoctoproject.org/cgit.cgi/poky/commit/?id=8bef99d3c85f48ff409eaebb964b1c45b203bdcf (there is cleanup in the following patches)