kev999,
After switching back to my standard 48/36 setup, I had the transport failure again with the same project.
You are correct, the Audio Engine is off. Clicking on it does nothing. I didn't find any solution apart from changing my default settings in Preferences back to 96/32, closing SONAR and restarting.
The RME UFX is a great piece of equipment but it doesn't seem to like sampling frequency changes. The Fireface 800 I had previously was similar. I guess that's at the heart of it, but I still don't know why the transport / audio engine off problem started happening with this project, as I've been working on it for more than a year.