To get the lightmaps to work you have to do this:
So if I make a ship look like a pin cushin it lights up?
:p
No!!! Lol hehe
You have to use the same texture as the texture used as the diffusion map for the illuminatin map, make sure it's using the alpha channel and then tick the 'color' box (red circled) under the title of self illumination and set that to white. Then it will glow on the alpha map.
The 'pin cushion' effect is from having a lot of hardpoints all over the hull, plus the scaling of the mesh.