If you are referring to your Hunter irrigation control panel, I would try to reset the panel to the factory settings and reprogram the system. This is how you do it:
"Press and hold the PRG button. Press and release the RESET button on the back of the front panel. Wait until the
display shows 12:00 am. Release the PRG button. The controller is now ready to be reprogrammed."
I don't think the whole house surge protection system has anything to do with your irrigation system. The Hunter control panel is warranted for two years, but I don't think that includes labor.
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