As you replied here regarding OS simulation error, there is another issue that you can check with the same grasshopper file I posted there.
The point is that when you add an atrium as an instance in the center of the building (atrium is taller) , when you do intersect masses, honeybee can not distinguish exterior walls as it should, but when you put an atrium on the side of the building it recognizes the separated exterior walls properly.
Regards
Amir
