Last question first: I think I would use a Composite material instead of a Mix and put a set of pure black and white outlines on top with a simple mask and stick it in the Diffuse channel.
As for the render itself, have you checked the Render Settings to make sure you don't have "Overwrite Kernel Settings" enabled?
For trouble shooting, I'd put your material on a sphere in an empty scene with a single light source & floor and see what you've got. Then start disabling segments of your shader. My guess is the problem lies in the SSS and your scene sampling, since all the other elements look to be rendering the same.
Also, while your at it, it's generally not a good idea to share a node between shaders, like you are doing with that bumpy normal map. Sometimes it works fine, others it causes odd problems.
This might give you some ideas. That's a MAToon.OSL node generating the outline. There are other ways to do it, but that's simple and easy.
