I have had similar issues, as in attempting to create a new template. When I design the model it can do mostly a simple floor and I have to complete it with the grow walls tool.
For instance, if I were to say add inner walls or try to create a complex structure I could not have a floor placed. The slab tool does not recess the build so it places the slab on top of the terrain and the free standing wall tool randomly joins and/or places the build zone in odd directions. When I tried to build a pagoda; I placed the slab, drew 4 corner sections and built a roof on it. However, when I tried to build the object it overlapped build areas with the slab and could not complete. When I tried to erase or remove it the structure sat untouched and the workers stood around it like an effigy to the gaff gods.
It would be nice to have a stand alone builder for the in game creation engine so I can tool on it in my second monitor while the villagers toil away at my tasks.