You would need to set up separate UV channels/textures for your diffuse and for your lightmap. This is really easy in Blender - first unwrap the model, preferably start with the diffuse, but it doesn’t matter in the end - then, in the Mesh Data panel (Blender 2.53) or Editing Context (2.49b) you will see the text “UV Texture”. If you have unwrapped, this unwrap would go into the the first channel. If you click the New/+ thingy you are instantly provided with a new clean non-wrapped UV channel. Bake your lightmap into this one and import in Unity, and it will be all fine and dandy.
Ok I import my model from Sketchup into Blender as a 3DS file.
This way all my textures from SU come across into Blender. I add spot lights in Blender - shadows are created.
So I click on floor of my model - which has a tile texture on it.
I go to edit - select all faces - click ‘u’ to unwrap - choose unwrap(smart projection) - and then go to Edit UV Image - add a new image - press Full Render - and get all my shadows and textures etc. I save this.
When I load my model into Unity and use this in material/texture for the floor it tiles on me.