I think I hear what you are saying. I must ask you a seemingly simple question. How do you know that you don't have any other start times on Program A,B,C? This answer may explain a lot. Are you sure that you have seen all of the start times on program A,B,C? Or are you coming from the position "I didn't set any start times so there must not be any start times". What is the Brand and Model of the Clock?
Some clock are inherently customer unfriendly, and if you have one of the few particularly unfriendly clocks you will have it set wrong and think that it is right.
The great thing in your situation is that you understand that there is a problem and are in the right place to get help. I can't speak for Arizona drip. I am Texas, but I have seen far too many people not familiar with their Timers think that they are programmed for one situation and the clock will reveal its own issues, but you have to go through the step by step. Maybe you already did all of this and my comments are a waste of your time, but in my humble experience the problem is going to be with the programming of the clock and the difference in what you think the clock says and what the clock says.
Bottoms up in Houston.