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The problem is that it is difficult for the software to calculate a temperature result when the flow is "off." So there is not a good way to arrive at some sort of average temperature over flow cycling. It does mean that users need to be careful how they interpret state data reported for such nodes, but the energy impact on the zones is being done correctly. This is part of the reason that the so-called On-Off fan is only used for self-contained unitary system models rather than being handled in a general way for central, air loop HVAC systems.