Question
It seems like either all of my zones go on simultaneously or it has 2 going at the same time.  It doesn't want to change from one zone to another. It just keeps the previous one on and turns on another.

Answer
I think you have serious problems with your controller.  You can try to reset it by removing the power supply for 3-5 minutes, including the battery backup, and then reconnect power.  Also try cleaning the circuit board with some canned air and a very soft brush.  If this doesnt help, consider replacing the controller.