I've never tried using an architectural material this way but your problem could still be trying to bake a luminance map: just having a black/white map for windows is not the same thing as a fancy glow map that has illumination cast at bits of the hull baked to it. For that you still need to bake a complete map. So I guess the question is, what type of a map are you using in the render to texture dialog?
Sorry if I misunderstood something again, but if you're using anything other than complete map this is still most likely the cause of your issues, architectural materials or not. A luminance map will attempt to capture just the lighting information into a texture. A complete map will do what the name says.
For example: say you have a a window glowing in a hull. The only thing you need from a glow map here is a black map with a white rectangle where the window is. But say you want a spotlight illuminating parts of the hull with a nice falloff effect? If you bake a luminance map you'll get weird results in the game. If you bake a complete map it will pretty much bake what you see in the render to the corresponding uv's of your texture. The game will pretty much override your diffuse/specular and make your lit parts look like in the render this way. If you attempt using a black/white glow map there you'll get a weird white non-transparent spotlight instead of a nice realistic looking one.
