An update:- the auto-meridian flip all worked fine in my sequence. the mount waited to track to my limit and then flipped fine.
So not sure what happened last night after the strange 'user.config' event with the new beta, but all seems well now. Only thing to check is the End of Sequence park, roof close and ccd warm-up which I'll see in the morning (or if I wake in the night - funny how this can happen when you're anxious 
).