To answer my own question, because MythTV logs in automatically, so you dont get the option to run it in a terminal. I got around it this way.
enable ssh server
log on using another computer, ssh -X -C mythtv@insert.ip.here
now run mythtv-setup from the console.
I have since given up on MythTV, it's interface is awful, and missed half my recordings. So back to a buggy Vista for me.
