Definitely agree with wetboots on checking resistance. Also check voltage coming from your master valve/pump start terminal at the controller (one lead on MV/PS and the other on common while a zone is on.
If 24 volts is present at the controller, then check the low voltage wiring at the relay.
Some models of Toro controllers also allow you to turn off the MV/PS for an individual program. Something to check out anyway. I believe the Custom Command, TMC 212, and TMC 424 have this option.
I asked about location of the relay to try and get a better understanding of the amt. of low voltage wire between the controller and the relay. Lightning has a way of frying wire and it's connections. Still not certain if the relay is next to the controller, or 100' away.