The alpha channel in the lightmaps texture is used for the engine a a shininess map, that uses the main UV map index, treat them as separate textures, if you wan't to see how is the LM texture in reality disable the alpha channel, same as the shininess map, if you're using PS goto the channels tab and click on the alpha channel, this way you can see the grayscale map.
What you have to do is make a shininess map, in greyscale (black=matte, white = shine) usually by hand
select it and paste into the alpha channel of the lightmap.
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