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The 90.1-prototype models are under continual maintenance. There are also some known differences between EnergyPlus versions. If you are trying to exactly match the published values, make sure to use the same version of EnergyPlus used to generate the results. I suspect that is the source of the discrepancy you are seeing.

Buffalo and Toronto have a similar climate. However, Canadian building code is somewhat different from ASHRAE 90.1. If you intended to model how your green roof model interacts with building code, you will need to use the NECB version corresponding to Toronto. However, if you are just trying to validate your model and come up with comparative savings estimates in this climate, then using a 90.1 prototype model is fine. The differences you show in your model are within the noise typical of weather and variability among buildings of a similar type.