QualicoreHomes

Yes, I've had that happen to me.  For me usually selecting "balloon through ceiling above" for the main floor wall works.  I did it on your TestPlan and that seemed to fix the missing drywall portion.  I did have to manually shape the porch wall above the roof the get the exterior wall to build correctly.  There are probably better chiefers that can explain exactly why it happens which might be more helpful.
 

To me it looks like some of the foundation walls do not align with your main floor exterior walls.

I copied the roof material and then adjusted the horizontal offset in the "Define Material" so it only moved metal from the one roof panel instead of moving it on all the roof panels.