Did you do any lawn work that would have disturbed the wiring to the valves? If two wires are now touching they will both open.
Maybe wires in the valve box are touching
Do you have a master valve? Maybe one valve is stuck in the open position. If so take it apart and clean the insides.
Nothing changed recently that would cause such an issue with the wiring but I did take a look- no wires are touching.
the Intermatic controller is one made to control an indexing valve, and it is the indexing valve that is your problem, most likely.
Had to Google indexing valves...
I suspect that you may be right. Odd that it only occurs when it's being run by the timer, though. I did find a helpful video on how to change out the stem & disk. The way my is installed is going to be very painful to replace- the water pipe leading into the valve is above the screws to open it. Mine also has a rotating stem at the top that allows me to go through the zones manually. I did pull that piece off & reseated it- doubt very much if that is going to resolve the issue though.
Thank you both for your responses. I've set the time so that it will start in the morning tomorrow- that way I can perhaps get a better idea on what might be happening. I suspect I'm going to have to bite the bullet & pull it fully apart to repair it.
http://www.autolawnsprinklers.com/wordpress/2009/12/replace-stem-disc-index-valve/