Have you already submitted a support ticket for this? If not, here are some suggestions:
– Double check the wiring: common wire goes to COM terminal block, and each zone wire should go to an individual zone port.
– I am not sure what you meant by ‘zones 1 and 2 use the same sprinkler head’ — are zones 1 and 2 sharing the same wire?
– How did you run a test program? Did you click on a zone and manually turned it on, or did you create a test program and start the program manually? Once the test program is started, what did the homepage show? Did it show one of the valve running?