Adding Cupla affects entire plan

[BB boy]

I am not sure anyone really understands what's going on? If I start from SCRATCH with a new plan, draw first floor, build roof with gable ends, the FOLLOW the cupola tutorial, I have no problem building it just like I WANT IT, and with either style roof. It is only when I open my original plan, and follow the tutorial: Build Floor> Blank 2nd Floor> draw ONLY the cupola walls on the 2nd floor> open the rooms dbx >make it open below> go look at a perspective then everything is screwy. I did manually draw the walls back in that would be the attic gable walls, but I have to remove the gable vents first, then add them back.