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The function that performs this calculation is here:
https://github.com/NREL/EnergyPlus/blob/9814fa5069b4cf52457ff0f9d18c7422f83eb33a/src/EnergyPlus/ThermalComfort.cc#L2442
Whether the zone is occupied is determined here:
https://github.com/NREL/EnergyPlus/blob/9814fa5069b4cf52457ff0f9d18c7422f83eb33a/src/EnergyPlus/ThermalComfort.cc#L2216
Basically it adds up all time periods that any zone is outside the range of the threshold (which is 0.2 C unless specified by the user) during occupancy.
A few things to check:
Are you using hourly values,this may not match up because the algorithm does this for each timestep.
Occupancy is when greater than zero
Heating and cooling times are calculated separately
Heating not met is when colder than the setpoint minus the threshold
Cooling not met is when hotter than the setpoint plus the threshold
You also should think about checking against the output variables:
I hope this helps you figure out the difference.