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If you take a hard look at illustrated DOE-2 help entry for PVVT, you'll note that PVVT will not respond well to simultaneous calls for heating/cooling when occurring between the control and slave zones. It is only listening to the assigned 'control zone' to determine (a) heating vs. cooling operation and (b) the amount of conditioned supply air volume available.

One system per zone is an option, but may result in equipment capacities well under what's actually available for custom curves (if I"m correctly guessing which manufacturer you're using)... Another means to avoid this issue is to regroup your PVVT system zones so that you have one system per set of similar load conditions (i.e. skin exposure / occupant scheduling). This should minimize simultaneous calls for heating/cooling within the same system.

Another note: For this exact sort of troubleshooting, you might find it much easier to highlight the top of the component tree under the airside HVAC tab, then to click the 'summary' tab immediately after a simulation. This display will assist you with pinpointing exactly which zones are having substantial unmet heating/cooling hour troubles in relation to their parent systems and by zone group.