When I use a texture with alpha channel for have different translucent values in it (like windows) the problem is that you can't see particles of weather or normal emitters behind the texture. ... If I use a translucent texture I can see the weather effects.
In this picture there are two windows, the left one use alpha channel and the right are a normal 256 color pcx with translucent, as you can see there is a emitter and a weather emitter in the other room, that are invisible in the alpha channel window.
