Baseboards in sunken room and Weird Floors

[JTabarlet]

I have two problems that have just come up.

1) I have a sunken living room in my current house and in the remodel design (Home Talk Forum was enormously helpful in helping me to design this). However, I cannot get the Bone White color that I'm using for the baseboards to go across the areas where hallways or other rooms butt up against the sunken floor; the baseboards appear the correct color only where full walls exist (see jpg file). I've tried using soffits of the correct height, width and thickness, but for some reason they don't work; they end up being about two inches too high and I can't change them. This isn't a huge problem, but it does bother me.

2) This one is more serious. I recently changed some exterior walls because I realized I had mis-measured the dimensions, making the house slightly larger than it really was. It was only a foot or so, no big deal, but after moving interior fixtures around and changing the wall dimensions, the floors looked odd. "Weird Floors (and ceilings) 2" shows the lovely grass now growing in my kitchen and breakfast nook and an unintentional vaulted ceiling ("Weird Floors (and ceilings) 3" shows how it was before the change). By the way, the floor materials on the room dialogue is set correctly (to "natural oak") and the ceiling is set to ceiling above this room. "Weird Floors 1" shows the floor in my den/media room with some tile and some wood; "Weird Floors 4" shows the earlier version. What's up here? Have I messed up the foundation?