Question-and-Answer Resource for the Building Energy Modeling Community
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As far as I can tell, AirLoopHVAC:UnitarySystem was introduced later and is supposed to be able to represent all the older AirLoopHVAC:Unitary... systems. I'm not sure why exactly the older objects remained in EnergyPlus as they are supposedly antiquated.
If you set them similarly you shouldn't see a difference in energy usage. Your problem might come from a whole lot variety of problems.
Anyways, what follows is not the answer to your question, but hopefully it should be very helpful nonetheless for your underlying goal. There is a project undergoing to create all the DOE reference buildings in OpenStudio using measures. This is available on Github, and is called OpenStudio Prototype Buildings.
It is not a 100% complete project as some building types are missing - such as MidRiseApartment - but the ones that are in there do work. For now you can just put the entire repository in your C:\Users\...\OpenStudio\measures (or wherever your os measure folder is located) folder and use it on a blank model in the OS App using the 'Apply Now' function.
