I think I've found a problem when creating a custom terrset. When I had problems with it, I dropped back and used the custom 'wire frame' set you've seen many times before and now it too is porked in the same way.
Atlas 1, types 0 & 1 appear good, as do Atlas 0, types 0,1,2,3. But all the rest are in shadow on a perfectly flat terrain. I can send the terrain to you if you like.
Luckily, the Make Map feature mirrors what I see in the editing window. SEE the jpg.
Here are the Atlas text files:
atlas,
512,ImageSize
4,ChannelCnt
4,rows
4,cols
texsrc/dunes.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp (notice that all of these use the same tiles and textures)
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/yellow508.bmp
texsrc/white508.bmp
atlas,
1024,ImageSize
4,ChannelCnt
2,rows
2,cols
texsrc/wireframe1016.bmp (notice that all of these use the same tiles)
texsrc/wireframe1016.bmp
texsrc/wireframe1016.bmp
texsrc/wireframe1016.bmp