I tried that as well kol, but it stil doesn't work, I had big 256x256 textures of tall skyscrapers from a sky tga, and I erased the skypart and replaced it with solid pure blue so I could have realistic looking buildings from a distance.. however in Wally even though the texure color was pure blue (0, 0, 255) with a "{" in front of the name.. I could'nt get the blue to appear transparent... This has happened for a lot of mod makers such as the makers of "Redemption" In it there custom textures appear to be using the "texture, 90" effect, instead of the "Solid, 255" effect.. so i take it they had the same problem.
Somebody more familiar with this should make a fool proof tutorial here..
Its a very common mishappen.. and would be use very much.. even from advanced mappers!