Thanks for your quick reply and explanation Jasem.
I tested the goto command after a test target passed the meridian and it worked as expected.
I chose another target and set auto-flip if passing 0 degrees and that worked as expected.
I created a imaging session which ran and after it completed the auto-flip worked as expected.
It seems when I watch it then it works correctly.
I'll keep an eye on it. Now that I understand that the hour angle tells me when it will flip I can watch it for the next few targets.