OK, so you can mark the "Accept as Solution" button if you like but I have to say that I feel like you didn't actually read what I posted!
I was able to do everything up to the point of Lodging the BAS with the ATO via MYOB software.
I will admit that I attempted to do this on a Sunday (which has always worked in the past) but with a little googling I noted that the ATO were doing some sort of 'maintenance' which was due to be completed on the Monday morning, I suspect this was the problem. Please note, that I didn't find that piece of information until after I posted the question.
Your instructions must be the genius addition because I have no idea how to "Update from ledger" so you would have needed to supply more information there and I did mention that I have been doing this for ages and there is absolutely no reason for the Software ID to change?? It has been that way for at least 2 or 3 years, ever since I moved from MYOB AccountEdge to MYOB Essentials Business??
I am curious how this would change?
End game: I signed out and tried the next day and it worked fine. I feel you probably wasted your time typing the below response. Sorry, but the help was far too little and 24 hours after I needed a solution anyway had I still been having issues.