I will try to address these one by one as I have not been on in a while. Thank you all for your time.
DAGHBOUJI, the configuration wizard already was run after the upgrade. A DNS alias is not changed in the SEP configuration wizard, it is changed in DNS
SameerU, we have tried this on multiple remote computers already running different versions of Java and also tried reinstalling Java on one of the remote computers and this did not resolve the issue.
jfschafer, respectfully your statement about port 8445 being new in 12.1.2 is incorrect, it has been the reporting port for long before this in 12.1 (possibly since the beginning of 12.1), to my knowledge, at least since our first version installed (12.1.1000.0157). It is even mentioned in the training manual put out in 2011.
The issue is not logging in with the IP Address or FQDN, it is logging in with an alias assigned in DNS that does not work properly. It is not a DNS isssue as the server would not be able to be connnected to at all if this were the case. Also, as I mentioned above and others have as well, this worked PERFECTLY till after the upgraded from 12.1.1101.401 to 12.1.2015.2015. It is not a firewall issue either as no ports have changed.
I never heard back from our Symantec Engineer about this. It would be great if a Symantec Employee actually looked at this. Aliases are not necessary, but they sure make remote administration easier as a SEPM can be changed without necessitating a change in how an administrator accesses the web console or java console, both of which encounter this issue.