I have a Minecraft scene, and within it the rig set-up uses alpha channels as second layers. This creates an issue when I render out the scene: http://i.imgur.com/qIzqGOQ.png
As you can see, the area surrounding the character (where the 2nd layer alpha channel is), DOF absolutely does not work. I've had to fix this in the past by doing the extremely laborious task of rendering out the character in one render and then rendering out the world in another, then combining the two in photoshop.
Unfortunately, I can't say I'm experienced enough in Cinema 4D to know if this is a widely known issue, or if this even makes sense to people who don't use Cinema 4D to create Minecraft animations. If this is the case, I apologize, feel free to disregard this post.