My issue was trying to login to ECP through OWA was not possible unless the Admin has a mailbox. In our domain Admins are not aloud to have mailboxes.
We tried recreating Virtual Directories for Front End and Back End for ECP and OWA. Ran the Updatecas and updateconfigfile scripts. After doing so we did not have any success. We also tried to use the Setup /mode:Upgrade command but it failed due to a service not being able to start. (Yes.. we ran iisreset a million times)
We eventually came to the conclusion below -
It was discovered after running "Get-Mailbox -Arbitration" we saw that there were no System Mailboxes.
Using the link below we recreated the System Mailboxes and were able to login again. The Admin issue was occurring on both Email Exchange ECP websites. I believe because they both work together, that these System Mailboxes are shared between the two.