Room Divider tool resulting in framing exposed?

[ChiefuserDRB]

I am attempting to create a loft in a pool house and am wondering why the floor keeps coming out with these exposed framing sections. Am I using the wrong tool for this? I created a second story, used a room divider then adjusted the opposite room to "Open Below". I also found that soffits, shelves and moldings dont cross over these places where the room dividers are and it has me puzzled. Is there a setting I have missed or am I going about creating this wrong?