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I am not sure how you calculated your first energy results. If you were using the model that was provided and didn't change anything and looked at the energy usages then these aren't the loads, these are end use energy with all the inefficiencies included. The ideal heating loads object does not include inefficiencies, it assumes that everything is working perfectly, no heating and cooling at the same time, boilers and chillers have a COP of 1 and so on.

The other thing you might want to check on is that the amount of outdoor air your model is bringing in is the same in both cases. This could also be causing some discrepancy.

These are my first two thoughts. I hope they help a little bit.