Managed to sort it out, there was a problem with the listener, the listener.ora file was just wrong - which is strange because when I went in to OEM stand alone I could look after the database.

Anyway, I created a listener.ora file on my local laptop (pretending I was on the Linex machine) using configuration assistant, and copied the file to the Linex box, stopped and started the Listener and stoped and started the agent.

The portals database now shows up in my service.ora file, and I can see it through Management Server.

Thanks to everyone for there help.

A