Eric might want to weigh in here, but I think that Toon III catches these objects because it's a post-render effect, whereas Toon!Pro seems to be one that works kind of during the render.  I'm no programmer or expert, but Toon!Pro affects each render square, whereas Toon III does its thing at the end of the render.

And if Eric does weigh in on this, maybe getting Toon!Pro (and Wireframe Pro, apparently) to recognize replicated objects would be a good thing to think about?  For most of my situations I've been able to just create instances, but it does load up on the geometry in a scene!

Thanks!
Dex