Hi Jay,
One thing that could be a problem is the stop time. Do you want it to run until 3:30 PM? In which case it should be set to 15:30.
Starting at 2:00 and running 2 zones for 60min in sequential mode would take it until 4:00 to finish and it would only run once.
There could also be a problem with the irrigation timeline display on the Home page but that should not affect the operation. I am setting up a program as you described and will be testing it. Thanks for the detailed description.
Dan