Rafters - Bird Mouth - Dialog Boxes

[rockinrandy]

ROOF - Wall and Ceiling Connection - Bird's Mouth
I figure these all work together.  I am trying to make sense of the roof framing dialog boxes.  We will be using 2x12 rafters on 2 foot centers.  I calculated that I needed a 2 1/4" x 5.5" Birds mouth notch at a 6/12 pitch to get my rafters to match up with the inside-top of the framed wall.  I think I am doing it right but my 3D views of the interior still look as thought the rafters aren't notched and I am getting a shelf at the top the walls.  Does anybody have a good explanation of how to set up all the dialog boxes?  Here are my settings:

Update:  Looking at the Roof Framing ( picture attached ) it actually looks like I have a much deeper Birds Mouth Notch than I think I have set up.  Any ideas about the proper set up?