Top surfaces of a print which contain layers above print very poorly. This is because it appears that Simplify3D does not include outlines for the surface layers to adhere to below the top layer. I don't really know how to explain, but hopefully some images will help.
I've gotten around this by setting up multiple print processes, and printing a few layers with solid infill before the surface layers begin to print. However, this is very time consuming for prints with many surfaces at different heights of the model.
Cura seems to avoid this issue by printing an outline of walls with the solid layer. Another solution, though somewhat less elegant and more wasteful, would be to print surface layers as a complete solid layer.
I've indicated the problem areas in the attachments.
*Edit: changed the title to better clarify the issue
