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McAfee ePO Web Console with custom SSL cert and problem with DNS

I have managed to get a custom SSL cert to work with our McAfee ePO 5.3.1 server. If we type the FQDN into the browser then we get the secure connection which uses the custom SSL cert from InCommon. However, in the browser I can type the servers IP address with port 8443 or the servename name like https://vbrhm:8443 and get browser message about invalid certificate. If, I do a nessus scan against our ePO server then it seems to find the non-fqdn name and therefore reports an unsecure cert as it is self signed and SHA-1.

I looked at the server.ini file and see an entry for "LastRegisteredServerDNSName". This entry does not have the FQDN but instead the servername. I have tried changing this entry to match the FQDN but it reverts back after the services are restarted. Is there something I have missing. I am wanting the server's IP address and Servername, when entered into a browser, to point to the secure custome SSL certificate and not the self signed one which is SHA-1.

Any ideas?