I've set up a scene in R12 using projection man with hand painted textures projected onto several objects. When I render the scene as a whole, the alphas in the materials work fine and everything that is supposed to be transparent is.
However when I try to render an object on its own to take into AE, the alpha includes the entire plane/object rather than just the painted elements. I'm sure I'm missing something simple but I can't seem to figure this one out. Below you will see the island rendered on its own with the incorrect alpha and then rendered with the other elements and appearing correctly in the scene.
Unfortunately I cannot. I don't own the artwork used to create the textures. I thought this would be a simple fix and I was just missing something. I'll keep playing with it some more. I might just have to export the scene to Max and re-set it up there. That is where I usually do all my matte work but I though I would give projection man a try on a simpler project like this one and see how it worked out.
It turns out that having DOF active in the render settings was causing the rendered alphas to display the entire objects rather than just the portion that had the texture projected onto it(see pics with original post for example)
I don't know if this is a bug or just the way C4D works but hopefully this will save someone else the two days it cost me:) Moral of the story is add DOF in post for your matte painting work.