Did you check Landscape demo that comes with Asphyre? It shows isometric terrain with multiple height. Does the same problems occur there?

The lines that are missing seems to be related to the "last pixel issue" I have been struggling with in Direct3D. Due to my major attempts to make software emulator compatible with Direct3D (that is, to make sure it shows the same thing Direct3D does), there can be slight differences in lines drawn in Software Renderer and Direct3D (in the edges - there could be differences due to rounding errors). However, Direct3D resolves last pixel issue in different way Asphyre does. Did you check the same application in software mode?