Bad lighting in automated builds

Hi guys

My team is using a headless machine to create automated builds of our project.

The build process works fine, however with Unity 5 it seems the lighting doesn't calculate properly:

A manual build looks like:

I've noticed that when I first load a scene in the Unity editor it takes a couple seconds for the lighting to calculate. I suspect that the automated build is not doing this step.

I have tried:

 Lightmapping.Bake();

But there has been no improvement.

Any ideas on how to get the correct lighting?

Thanks, Ves