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If your heating and cooling setpoint schedules for the design days include a thermostat setback/setup and your system is being autosized, the resulting capacities and flow rates may be way oversized because the autosizing routine is trying to enable the zone temperature to jump from the setback to the setup temperature in the space of a single simulation timestep. If this system is then run under normal operating conditions, the oversized capacities might allow it to meet the load in a very short space of time, and depending on the size of the window used to determine the peak, you might see funny numbers.

The behavior you are seeing for the night cycling vs. follow HVAC schedule makes sense if the system is oversized. If night cycling is enabled, the zone never gets more than 1-2F above/below setpoint before the system cycles on, at which point the load is pretty low. If the system is scheduled off at night, then when it comes back on on Monday morning, the zone temperature is well above/below setpoint, and the load is much closer to what was experienced during the design conditions.