BTAxis is right, there's no need for an alpha channel for the glowmaps. MCR, it's possible that the alpha channel is the reason that you thought that the color intensity didn't matter. If you're using the alpha channel to change the "intensity," then the actual color values of the pixels haven't been changed at all, which is why it doesn't look any different in game. If you just work in RGB (instead of RGBA), you won't have that problem.