Automatically generated wall in the middle of house

So I have a 3 story house I'm working on... Basement, Main Level, and 2nd Story. I have this bathroom in the basement, from which automatically generated attic walls are being generated and appearing in the middle of a hallway on the MAIN level, inline with and just above the basement bathroom walls. I cannot get these walls to stop auto-regenerating, or go away unless I remove the basement bathroom walls. Why does this program think that the main level is an attic?

I agree with Glenn, your problem does not sound like an island room but without a plan or at least some pictures, people are just going to make random guesses. You should not turn off the "Connect Island Rooms" feature unless you actually know what you are doing and even then there is really no reason to. If you want to know more about why, then read my comments on this thread: https://chieftalk.chiefarchitect.com/topic/30870-mysterious-room-divider-can-not-get-rid-o