If the message goes away then it goes away. If I were a repair guy and I tried to fix your timer problem there would be nothing to fix as I looked at your timer. The no AC will be a problem if you saw it all the time. Do your sprinklers turn on and you see water. If they come on the system is working and you have no issue.
Good Luck. I know it is new and you want it to be perfect, It probably is.