So it looks like the problem was that you updated your DNS but forgot about TTLs. Your new cert has the correct name on it, but you didn't setup the cert chain properly (SSLCACertificateFile under Apache)
You are right. We changed our frontend from Django+Apache to Rails+Nginx, and we forgot to specify the certificate chain in nginx config file. Now I added the description, and confirmed that we can access to the web site via SSL.