Help withTransparenies

I am using FSPaint to make small modifications to textures. When loading the aircraft in FS after modifying the textures the windows of the aircraft are not transparent and appear solid black (as per texture page) although in the viewing screen in FSPaint they are OK. I am not understanding the 'RGB' and 'Alpha' channels/editing and FSPaint does not help me enough. Can someone help - Please?

it depends what program the model was made in (i think) that dictates what the alpha layer does. in gmax models the alpha layer is for reflection, in others it is transparency. make sure the alpha layer for the glass texture is very dark.