Zones not working correctly

I am having trouble getting the zones to detect the wall enclosures and dimensions. If I draw a square room and populate it with windows and doors, then add a zone, the program detects the dimensions and fills everything in. But if I add another adjacent room to this one, and try to add a zone the same way, it doesn't auto-fill, but instead asks me to draw out the zone manually.

and when I do that, it covers up the swinging doors and other elements. An example is below, where the room on the top seemed to function correctly, but the one under it required a manual configuration (which didn't work correctly). I tried zone dividers, but it didn't correct the issue. Any idea what I am doing wrong here?

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