I just went to try your suggestion, and now everything is working correctly, ie I can't recreate the problem. I wonder if it was a more subtle bug? ie I just got the unit, and the manual runs were the first ever for those zones, ie their was no run history. Anyway, I will re-post if the problem happens again.
I do believe I had tried the refresh when it wasn't working this morning. It was very strange, it still showed the status as counting down (ie time left to run in the zone). I also quit out, killed and restarted the app, and it was still counting down. The big difference now is when I press stop, I get a pop up message at the bottom of the screen saying "stopped running ..." and everything resets. I wasn't getting that message this morning and the stop button was still there (even though it had successfully stopped the zone from running.)