It is not stacking.  You probably have the pump connected to the master valve.  When you start a program and specify that you want to run it with master valve on, it'll turn the master valve when the program starts.
Now, if you run a program that starts the pump only for 2 minutes at the same time, it will start the pump, but aster 2 minutes, the pump only program stops and turns off the pump.  I think this is what you're seeing.
If you need to run a program with a pump on for the duration of the program, specify to run the program with master on.  If you need to run the pump for 1 minute ahead of the program, then start the pump only program 1 minute ahead of the other program.