Hi, everyone (and especially Eric and LawB10). Thank you for your inputs and ideas.
I experimented, and the issue appeared to be that the Open Below room type/space on the second floor (which forms the space above the stairs) had different Structure settings for ceiling height. When I adjusted the ceiling height to match all the other ceiling heights of the other rooms on the second level, the strange popup shaft disappeared and the roof re-aligned to where it should be.