1. You had to set an Ini setting in Oblivion to get map tile in color. The same setting is (sadly) not working in Skyrim. We have the same problem for our Skyrim map and have not found a solution.
2. In the partial black cells the water failed to render. This seems to be completly random and could be circumvented with multiple generations.
the completely black cells are either water cells (see above) or cells with very high meshes. The latter seems to be unrenderable.
We've found further issues: So there are sometimes tile without the meshes rendered. This seems to happen a lot if a mesh is placed on the border of a cell. in one cell the mesh is displayed in the other cell it is not.