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It sounds like your internal source construction isn't getting assigned to the right surfaces. Make sure your construction set has the default floor construction set to your internal source construction for 'Interior Surface Constructions' (your second floor surface should have a 'Surface' outside boundary condition) and for 'Ground Contact Surface Constructions' (to get your ground floor surface, which should have a 'Ground' outside boundary condition). You can verify the construction assignments for your surfaces in the 'Spaces' tab under the 'Surfaces' sub-tab.