Double check and see if the water is coming out of the heads. It's possible there's a mainline running through the grass that is leaking.
I've never seen a cracked seat on the valve in question. Look for a hairline crack in the seat anyway. That's the part the diaphragm pushes against. You did ask about flushing out debris. Check and see it the seat has pits in it. Sometimes you can use sandpaper to get the small pits out. Otherwise you'll need a whole new valve. As far as flushing goes. It depends. You can take apart the valve on the end of the manifold then turn the water on and off two or three times.
If I can't fix it, it's broken!