Of course, thanks for getting back to me.

After some trial and error the dual light solution does not work either. 

The root of the problem appears to be when Double incoming light is checked, SF is doubling the lightmap contribution. 

Is there a way to set up a control for how much of the light map SF mults into the result.

We need "Double Incoming" to only effect the direct light not the Light map.

Any word on this issue? I've run into the same thing.

From what I can tell Beast uses Unity's default shaders when it bakes and just pulls in the color or texture from the appropriately named value in the SF shader.

So if you are using, basic diffuse without double incoming light, Energy Conserving, or PBL, you will get very different results after the bake because the light values that your shader needs are blown out when applied to a standard shader.

The only solution I have come up with is having two sets of lights. One for baking and one for my shaders in real-time.