AnthonysToolbox, I also had the problem with Transparency on textures, but i had a talk with Gmah, And he found a solution for it. However it seems like he can't put it into mirrormachine, you need to manual adjust the wmo file in hex, and change the blend mode from 0 to 1. for the material with that kind of texture. As i don't have any Hex knowledge at all, i can't explain to you how to do it, but maybe Gmah can write down a short tutorial about it.
struct wmo_file/struct MOMT momt/
Once you found the texture you'll have to change the vlue of "UINT32 blendMode" from "1" to "0".