Godaddy SSL certificate installation problems - intermediate certificate not being recognized

domain = mail.gottfried.org
Installed both the certificate and the intermediate certificate from godaddy (used the 10.6 mac os x version)
Response from:
http://www.sslshopper.com/ssl-checker.html#hostname=mail.gottfried.org
The certificate is not trusted in all web browsers. You may need to install an Intermediate/chain certificate to link it to a trusted root certificate. Learn more about this error. You can fix this by following GoDaddy's Certificate Installation Instructions for your server platform. Pay attention to the parts about Intermediate certificates.
When I check in 0000_any_443_.conf
I see:
SSLCertificateFile "/etc/certificates/mail.gottfried.org.1E5F3C903B64E78E3241929B16F616D1DDD130FE. cert.pem
SSLCertificateKeyFile "/etc/certificates/mail.gottfried.org.1E5F3C903B64E78E3241929B16F616D1DDD130FE. key.pem
SSLCertificateChainFile "/etc/certificates/mail.gottfried.org.1E5F3C903B64E78E3241929B16F616D1DDD130FE. chain.pem
I am assuming that the intermediate certificate should be:
mail.gottfried.org.1E5F3C903B64E78E3241929B16F616D1DDD130FE.chain.pem
When I look at that certicate it is the same as
mail.gottfried.org.1E5F3C903B64E78E3241929B16F616D1DDD130FE.cert.pem
When I check keychain and exported both the mail.gottfried.org certificate and also the starfield secure certification authority they match what was installed initially (what I downloaded from Godaddy).
It looks like in the install process the intermediate certificate is not being linked to the ssl certificate and that the ssl certificate is being used for the chain.
Anyone have any suggestions?
I have talked to both Godaddy and Apple Enterprise support. Godaddy has nothing past 10.6 instruction wise (though the support person really tried to help). The Apple rep couldnt really help and if I really want help from them I need to talk to integration where costs start at $700....
Anyone have an SSL provider that worked properly with 10.8  or has really good support for mountain lion server?
Please let me know.
Thanks!

While you still can, get a refund for the certificate, and get a certificate from somebody else, and preferably one that doesn't need an intermediate?  That'll be the easiest.
If you're not doing ecommerce or otherwise dealing with web browsers and remote clients that you don't have some control over or affiliation with, you can use a private certificate and get equivalent (or arguably better) security.  Running your own certificate authority does mean you'll learn more about certificates, though.
Here and here are general descriptions of getting certificates and intermediate certificates loaded, and some troubleshooting here and particularly here (TN2232).  I have found exiting Keychain Access to be a necessary step on various versions.  It shouldn't be, but...
FWIW and depending on your particular DNS setup and whether you're serving multiple web sites, you'll need a multiple-domain certificate.
Full disclosure: I've chased a few of these cases around for customers, and it can take an hour or three to sort out what the particular vendor of math, err, certificates has implemented, to confirm the particular certificate formats and possibly convert the certificates where necessary, and to generally to sort out the various posted directions and confusions.  (I'm not particularly fond of any of the major math, err, certificate vendors, either.)

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