Question
I put on zone 1 manually and zones 1 and 4 go on. Zones 2 and 3 do not go on manually at all. The same thing happens when in the auto mode.

Answer
Hey Bob, you either have a problem with your controller, or a problem in the wiring going to your valves. To determine if the problem is in the controller, you will need to check your voltage on the terminal strip in the back of the controller. Simply remove the wires from the terminal strip marked #1, #2, #3, #4 and C(common) and make sure you mark them so you know how to hook them back up.  Now turn the controller on and  start with station #1 and check your voltage with a volt/ohm meter, touch the negative lead to the C terminal and the positive lead to the #1 terminal, and you should get a reading of between 22 to 26 volts. Also test the #2, #3 and #4 terminals and make sure you are "not" geting a reading when #1 is on. If you are getting a reading on the other leads, then the controller is bad. If you are just getting a reading on the #1 terminal, then  the controller is good. Now turn on #2 valve and do the same test as you did for #1. Likewise do the test for #3 and #4. Each time you should only get a reading on the # you turn on, if you get a reading on the other terminals that are not turned on, then the controller is bad. If you determine that the controller is good, and #1 and #4 run at the same time, and #2 and #3 don't run at all, then you need to check your wiring and make sure the valve solenoid are hooked up correctly, or your wires aren't cut or frayed somewhere. Good luck and have a great day.