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The EMS actuator for Mass Flow Rate Setpoint will typically act on a set point manager with control variable set to MassFlowRate. For example:

SetpointManager:Scheduled,
  MyWaterCoilMassFlowRateSchedule,
  MassFlowRate,
  some schedule name,
  VAV_1_COOLCDEMAND INLET NODE;

It doesn't matter what the schedule value is (in the "some schedule name" schedule) since you will override that value. I am surprised you did not get a warning. If you can't get this to work please email your input file to EnergyPlus-Support@gard.com.