Worked out what the issue was. On installation the certificates where somehow corrupted. Which meant only the ERA server machine was showing with an agent active.
Running and installation repair on the Remote administrator program resolved this, and the default certificates were recreated,
Was able to successfully deploy the agent to a target computer.
However, now the problem remains is that the ERA server which always reported it had an agent running. (but wasn't connecting correctly) refuses to acknowledge the bad agent install has been removed and will not take a pushed remote install from the console. So, I tried a manual removing it and reinstalling using the live installer and corrected certificate and it still cannot connect to the console. (I assume cause it's never really been able too.)
Really tearing my hair out about this now.
Is there some way to force the database to remove that it has an agent installed manually? Or is there any other solution?
thanks