Not sure, but it might be that you're baking with mental ray? If so, try setting the renderer to scanline or set the visibility for the low poly in object properties to 0.0
FYI the problem I was having was caused by one of my UV's being outside of 0,0 to 1,1. Fixed that and then the map converted perfectly. This tool is great!
You should be able to do something like this in the shader to fix it I think? if (dot (cross (normal, tangent), binormal) <= 0.0) { binormal = -binormal; }
I have the artbook for both 1404 and 2070 games and it looks as if they just model each building on a plane that has a alpha on it that blends with the underlying surface.