I think perhaps that we should be more selective in the certs we add to ca-certificates.crt. Debian has a configuration file /etc/ca-certificates.conf, and only adds certificates that are explicitly listed there to ca-certificates.crt.
Several of the certs in /etc/ssl/certs have comments like this: # alias="Bogus Global Trustee" # trust= # distrust=CKA_TRUST_CODE_SIGNING CKA_TRUST_EMAIL_PROTECTION CKA_TRUST_SERVER_AUTH # openssl-distrust=codeSigning emailProtection serverAuth So it seems that the NSS certificate store may include known-bogus certificates, perhaps to allow displaying a more severe security warning than the common case of an unknown CA (e.g. self-signed certificates). We should find out whether these Bogus untrusted CA certificates are present in Debian's /etc/ssl/certs, and whether they are present in its ca-certificates.conf. We should also determine whether OpenSSL and GnuTLS pay attention to those "distrust" comments (see above) in the single-file certificate bundle, and whether they pay attention to them in the smaller *.pem and hash-named files. I will investigate later today, but if anyone is inspired to investigate sooner and report their findings, feel free. It could be that 993300f6c and/or e979e6dd523 should be reverted. Mark