I think I've isolated the problem. If you make a cabin with the stairs enclosed in the cabin itself, the three roof tiles on the floor above those stairs will not register correctly, preventing the game from marking the floor the stairs go up to as interior. The issue can be worked around by having your stairs outside, or in a room separate from the rest of the lower floor's rooms, or apparently by having the stairs against an interior wall? The behavior still seems inconsistent, but it does seem to be caused by stairs.
