If water was coming out of all of the heads then all of the zone valves are open. Close the zone valves from the top handles (solinoids) as well as the small diamond shaped bleed ports. Do not close the solinoids very tight, firm is useally good enough. Most of the time when blowing out these type of valves, you just have to open the bleed ports to activate the valve. Sometimes they are left open for the winter. If you have trouble with turning them, you might use a screwdriver to vlose them, but be gentle.
This problem has nothing to do with your timer (clock).