Dual Lightmaps Broken with SF

Additional info: On further inspection it seems that this is due to SF not working properly with Deferred Lighting (disabling dual lightmaps still leaves the transparency issues.

Perhaps you could add dual lightmapping support for forward rendered shaders as hinted at here under the "Dual Lightmaps" section: http://docs.unity3d.com/Documentation/Manual/LightmappingInDepth.html

It would be extremely useful to be able to have single lightmapped shaders able to receive dynamic lights and shadows (For a flash light effect for example) though I suspect this is probably only possible with deferred lighting.

Deferred rendering is a huge topic which has a whole set of cascading emergent issues and design choices needing to be done. It will be done, but in post-release, not now. I'm not sure if you can get dual LMs to work properly forward rendering, but I'll look into that in post-release as well :)