I've got the overframing blues and there's no way out

[GeneDavis]

One of these barndo projects, this one for a nephew with too many vehicles, some large.  The 2200 sf house that is attached to the car barn has a reasonably complex roof with gables and wrap porch roofs all coming from the central tall gabled roof with a 10:12 pitch.  Here is a birds eye view of the barn roof (4:12 all trussed) laying over the barn-side roof of the house.

 

While the barn is all trussed, the house roofs are all stickframed, and the lines you see are the rafters ghosting through the sheathing and roof finish.  This thing has a couple features of the plan that are (I think) throwing kinks into my setting of roof planes and the rafter framing for each plane.  This image shows the 10:12 roof part of which is under the overframed barn roof extensions above.  That there is so much of the 10:12 being raftered is due to the rafters framing the vaulted ceiling (one half of it) in the greatroom-kitchen large open room below.

 

The barn roof has a different framing scheme than what lays over the house, and the planes that are built atop the house are not all stick framed to the same rafter depth spec, thus there is the one single plane in the foreground, and beyond that, there are two planes, one highlighted, the other not.  It took me hours of fiddling to get the planes coplanar with the garage roof planes, but that done, I am unable to properly frame the near plane.

 

That plane is entirely over the 10:12 pitch roof below, the lower roof framed in 2x12.  I have the layover plan specified as 2x10 rafters and when rafters are either manually placed or autoframed, they are identified as 2x10 but are chopped to 2x6.  Is this a known glitch in Chief when stickframing one roof over another?  This roof has actually TWO roofs under, the vaulted roof half I had to do as a roof instead of a ceiling plane and framed in 2x8, then the 2x12 main roof over that, then this barn roof overframe.  A three decker.  Here is a pic of the framing.  That layover is supposed to be showing 2x10 rafters but Chief has 

ripped off the bottom of each to make them something close to a 2x6.