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The key issue is that EMS sensors are getting information from output variables or meters, which are updated near the end of each timestep. If you were to add an EMS output variable for the EMS sensor value and compare that to the Plant Load Profile Mass Flow Rate output variable that it's connected to, you would see a lag or delay of one timestep.
So, if you're trying to use an EMS actuator to update the pump mass flow rate, which is normally solved for by EnergyPlus in an iteration loop at the middle of each timestep, that actuator is making that change based on an output from the previous timestep. You can read more about the sequence of what EnergyPlus is calculating each timestep in the Program Calling Point section of the EMS Application Guide.
You can read more about this in other Unmet Hours posts here and here.