Mono's TlsTest file is really good at checking this out, so it seems a bit silly to even ask - but: Can you use WebClient to query the .svc file and get an answer? If not, for some reason, you probably still have problems with the certificate.
I also suggest that you used mozroots or certmgr to test the root CA? How about explicitly adding a certificate to your site in the repository through certmgr?
Another reminder: certmgr usually works with a copy of certificates for the current user, you need to specify the --machine argument --machine that all users receive the certificate.
Goyuix
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