Hi,
To start off I am using 2012, but don't believe that makes a difference unless it is a program bug.
I have 3 assembled floors, Basement and foundation, Main floor, and Second floor. When I use the reference circle on the three plans like I think I should, then the lowest wall on the main floor sits down on the footing of the foundation at the point where I put the reference circle. (see foundation into main floor)
Now I have noticed that when I delete the reference circle on the basement that it all looks pretty good. The walls SEEM to sit on the foundation, but on closer inspection I find that the walls are hovering 3/4" above the foundation wall. (see other two images)
The reference circle is on a corner of the house that is at a 30deg angle. Can that make a difference? I have copied and pasted the walls into a completely new project and it does the same thing.
Wes