No not every system has a master valve. There is almost certainly an error in the clock programming like mike has said.It looked like the "TOTAL CONTROL CONTROLLER" has a programable ON/OFF MASTER VALVE per program feature. I have never seen one of those clocks around here,but maybe you can reset it. I assume that it doesnt come from the factory already set up for a master valve,most systems do not have one.
I take that back im looking at the manual for that clock now,it says
MASTER VALVE/PUMP START ON/OFF
The Total Control enables automatic operation of the Master
Valve/Pump Start output circuit to be controlled independently for
each watering program. For example, if a program is used for drip
irrigation and the system pump is not required, the Master
Valve/Pump Start output circuit can be shut off whenever that
program begins operation.
The factory setting is
ON for each program. Use the steps below to
select the operation of this feature for each program as necessary.
1. Turn the function dial to the
Station Times position.
2. Select Program
A, B, C or D with the Program switch.
3. Press the
NEXT button repeatedly until MASTER VALVE is
displayed.
4. Press the
OFF or ON button to display the operation of the master
valve/pump start output for the selected program.
5. Repeat steps 2 through 4 for each program as necessary
hope that helps you out