The first issue that came up was that the Certificate was not recognize. I saved this to my machine and imported it to all tabs of the Certificate Authority. I also realized that the link being used didn't have the FQDN. When I entered this it seemed to correct the Initial Certificate Error which was thought to be the issue.
As it turns out this wasn't the case. When I log in with the Server Administrator account and I try to go to ; for example; the Security Link. It will send me immediately to a log in page and I would have to enter the credentials again to proceed.