So I'm having the same problem that this guy had: Shadow Map Issues, AFAIK, exactly the same.
Basically this wall is made up of repeating meshes. When I run lighting, the lightmap from one mesh (eg the 4x2 panels in the bottom right) is applies to another instance of that mesh (in this case just above it). Weirdly, it doesn't affect all the instances. Just a few. Even If I delete these few 'problem' meshes and add them into the scene again, it's as if the same one's suffer the same problem.
All the meshes have two UV channels with unique UV unwraps. All the meshes have the Lightmap set to slot 1 and diffuse to slot 0. All the meshes have either a 512 or a 256 lightmap. I have tried different lighting quality levels.
I'm at a loss here, Even when I delete the meshes and put put new copies in the world the problem persists. Any Ideas?