Sorry I'm kind of at a loss, but I have one suggestion.
Awhile back I had painted a nice texture on a map of mine with Ed42. I brought it into battlecraft for shadow generation, but some tiles would be good, and others awful looking! The good tiles were what I had painted with shadows, and the bad ones were battlecrafts crappy generated textures from the material map.
Try this (Hopefully you weren't the one who suggested it to me, lol):
1) Open the map in BC with your nice textures
2) Go to the paint menu.
3) Go to every 'piece' of the texture (individual texture files really)..you should know what I'm talking about. Use the smallest brush, and set it to 'darken'. Just brush a little bit on each square.
4) NOW generate shadows how you would normally...then merge. HOPEFULLY you will have your new texture.
Like I said, I'm kind of at a loss, but maybe this would do it..?
