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I would speculate that you didn't adjust wind speed for height above ground. The weather file wind data is usually for a 10 m height above ground. When apply this model, EnergyPlus will adjust this speed for each zone in the model based on the height of the zone's centroid, 1.5 m in your case. The setting of Terrain in the Building object has an impact on this adjustment -- see the section in Engineering Reference called Local Wind Speed Calculations
You also don't mention how you dealt with the stack part of this model, so that could be a factor in your comparison.