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As you suggested in your question, the night cycle manager is always lagged by one time step, so the zone temperature must fall beyond the availability manager "Thermostat Tolerance" for one zone time step, and then the system will come on at the next time step and run for the specified Cycling Run Time. You thermostat tolerance is set to 0.2C which is also the same as the tolerance for the thermostat setpoint not met outputs. So, you can reduce the number of unoccupied hours not met, but making the Thermostat Tolerance smaller in the availability manager, say 0.1C. But there may still be times where the space is heating up fast enough to be 0.2 or more beyond setpoint in a single timestep.