Question-and-Answer Resource for the Building Energy Modeling Community
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Besides what answered by Eric which is very helpful, I'll suggest also running an extra simulation with IdealLoadsAirSystems to eliminate any impact brought by different hvac systems (Mostly I'm lean to trusting this number to be loads as my understanding).
The predicted sensible load variables you're looking at are still dependent on hourly zone temperature, so if your hvac systems are not conditioning zones into exactly the same temperatures every hour, the numbers might vary. So if in your case even annually aggregated load numbers are very much varying, you might want to check hourly zone air temperatures for both systems to see how well the setpoint is maintained.
Hope this helps.
