Ok, the reason of your problem is that the skins are wrong sorted.
The model that didn't work used two different skins for the two subsets of the mesh texture. So, there are two possibilities. Either you have a common lightmap for all mesh subsets. Then it must follow the mesh textures:
tex1,tex2,lightmap
Or you have two lightmaps, one for each subset, then the order is:
tex1,lightmap1,tex2,lightmap2
But in your model the common lightmap was the second skin, followed by an apparently unused skin, and then by a fourth skin used again for the mesh. The engine has no way to know that your second skin is meant as a lightmap.
This is maybe misleading in the manual - there is stated at some place that the lightmap is the second skin. But this is of course only true when the mesh texture is the first skin. I'll fix this in the manual.