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Without an input file to look at it is difficult to determine if there is an issue or not, but here are a couple of things to check:

• Double check that your AirflowNetwork:SimulationControl object is set up properly. It sounds like the simulation you want would have the "AirflowNetwork Control" field set to MultizoneWithoutDistribution, but I can't be sure. Make sure all those fields make sense in your case.
• Add output variables for the flow rate between zones along your network linkages to see if you have flow through your windows, etc. If those come up as zero, then something fundamental is going wrong.

I am puzzled as to why you are including horizontal openings in the situation that you have described. Those should be used for penetrations in floors or ceilings, not "regular" windows. It still might work, but you'd be better off going with one of the other openings if you are modeling a window-like opening in a wall.