It seems to me that Cycles Baking goes by the settings of the Render Layer at the top of the stack. I discovered this because I was trying to bake an object that was on Render Layer 3 and it kept coming out black. I then noticed that out of my 5 Render Layers. the top Render Layer had layer 3 ‘Excluded’. Once I toggle layer 3 back to being included, it baked fine.
This means that if you intend to bake anything, reserve your top render layer for baking and do your fancy camera rendering ion layers below that.
Have i observed correctly? Does anyone know anything more? Thanks.