Texture Atlasing Issue with Export Lighting

[pavior4871]

Hello. I'm having an issue with an outputted single layer lightmap.

The resulting texture packs my materials very tiny, with a huge grey space overtaking the texture. I'm trying to understand where these grey materials are coming from. I figured they might be from the other side of the faces which use the default grey; however, I have "Render Both Sides" unchecked, so I'm not sure if Lightup is still picking these up.

The wall in the screenshot is a single group, so Lightup generates a lightmap just for the wall, but as you can see, there is no grey to be seen on this side, just greens, tans, and browns.

Edit: It seems this section isn't exactly grey, but it's transparent and receives lighting. Can't figure out what would take up this space.