i have also noticed this. I used this to create the start screen i sent you, and it appeared all black in Image2Tex, even though it displays properly in game. One wierd thing is that it displays the transparency of stock TEX files, but ignores it in the ones i create. Maybe something to do with the image headers it creates?
Either way, as long as the first color in your indexed palette is the color you want to be transparent, you can ignore the way Image2Tex displays it. You also must save your image as a BMP(or at least i do) in your editor.
lee