I dont know !?!
Possible causes...
1> Texture you are checking is not the texture on the models. (re-import it into med)
2> The model has multiple "leaf" skins and you haven modded/shecked them all.
3> The models in WED are not the same ones as the "fixed" one. (replace one tree in WED as test)
4> There is a shader on the models thats "interfering" with the blackness of the skin.(remove shader)

Otherwise, I dont get it...
Can you post one of the textures, or even a whole tree model as a zipped file?