Summary: Some Gentoo systems have 2 (related) CA certs in one of the files in the standard root CA bundle, one of the CAs is listed separately in another file. This leads to problems where the same trusted root is loaded twice.
Working with a poster to the OpenSSL-users list, this was resolved today: http://marc.info/?l=openssl-users&m=123721072930382&w=2 there was a previous unresolved report of the same issue misdirected to postfix-devel: http://www.pubbs.net/postfix/200901/25273/ This post is for the archives. Not much more to say, the Gentoo (and perhaps other) distribution root CA bundle is slightly broken and with any luck will be fixed not too long from now. -- Viktor.