Houston, we have a problem! It sounds like you have anti-siphon or pressure vacuum breaker valves installed below ground. This is BIG no-no. That water in the box...nice water filled with dog poo, chemicals,etc. potentiall could end up in your kithcen faucet.
Anti-siphon and vacuum breaker valves will typically "burb" a little water during the on and off cycles. Also, if they are installed below the level of the heads on the system ( underground pretty much says it all!) then all the water in the pipes will also drain out of the valve at the end of the cycle.
If I have misinterpreted your set-up, tell us what kind of valves you do have and how they are installed.