I believe you are correct as I can also share another situation that backs up your assumption.
Previously I had the program set up so that the motor ran 20 min/hr. The program ran from 9 am - 7 pm. There were no problems with the motor being off at night, although I can't tell you the precise time that it turned off. I then needed to run the motor for a longer time so I changed it to 40 min/hr (9am - 7pm). The motor would not shut off at night. My guess was that the motor was running when 7 pm was reached. All that probably happened was that the program stopped but the motor was not turned off, regardless of how long it was running in the cycle. Since the program stopped running, there was no off command issued to stop the motor at the end of a 40 min cycle. I then changed the time to 7:21 pm to insure that the motor was off when the program stop time was reached. I will add a "off" command to Else.
Getting back to my original question - why doesn't the program take over after I manually intervene during the day?