i dont think you guys understand what an alpha channel is & how to use it for transparency so i will try to explain .
first off when you create an image its made up of 3 channels red,green & blue (RGB) .this will give you the full range of colours with which to paint your texture.
so you paint your window frame & glass texture on these layers.so for example you paint the wood frame a brown wood grain ,then paint the glass a dirty blue.
now thats the basic texture finished ,but we want the glass to be transparent so we have to add a new channel to the texture this is an alpha channel.
Alpha channels act as masks through which you can display images.alpha channels are 8-bit which means it has 256 levels of gray from 0 (black) to 255 (white). White acts as the visible area, black acts as the transparent area. The level of gray in between determines the level of visibility. For example, 50 percent gray allows for 50 percent visibility.
so in our alpha channel we paint grey into the glass area of the texture & paint the frame full white .now save your texture as .dds or .tga with alpha & you should have transparency in your texture.
hope this helps
cheers henry