I've restarted Publishing Tools, but getting the same error when trying a direct publish, with a new MXD. I'm not too bothered as long as publishing from the sd file works, but curious why that is that's still giving trouble. I did find the following in the log, not sure if that's pointing out:
Unable to connect to the identity store using SSL.
ArcGIS Server will revert to using a non-SSL connection to the identity store and credentials will be sent in clear text.
In order to use SSL, verify that your identity store has SSL enabled.