I remember reading a post about how one could get lightmapping to work by naming the nodes correctly. It sounds like this may have changed in the update to 5, however.

Joachim, if it's not too much to ask, would you mind giving a basic run-down of what's changed/why it's more complicated?

Thank you for the help, that solved it! 

Any more news on this topic? I'd love to have lightmap functionality on my custom shaders.

Update: The problem presents itself when any of the lighting/shadowing components are combined through an Add, Multiply, or Lerp. This problem appears to be more about the way the lighting components are combined than anything else. Still, it's behavior feels like a bug. Custom lighting only appears to work appropriately when recreating the Blinn-phong shader model. This obviously defeats the point of custom lighting by forces us to fight against the Blinn-Phong model. 

edt: Clarity