Adding a second floor to an attached garage

[David J. Potter]

...what am I doing wrong ?

Nothing, that is how the software is programmed to operate, that does not mean you must follow, robotic-ally that programming. Rather once the second floor is created (you should probably select the "Blank Second Floor" choice, and then just draw in the second floor walls where you need and want them, Turn "Off" Auto Build Roofs so the roofs stay where they are (if you intend an attic room) or not if you intend a full height second floor over the garage only.
You always guide the software to a result, you never follow or expect the software to lead to a result, you do the guiding and controlling.

DJP