Well, I'm here again. Still am not able to use ID passes effectively. Even the MILA matte pass built into the new mental ray render settings.

I've got a very basic comp with 2 copies of an image. Using the EXtractoR plugin, I set one to take all channels from matteA, and the other copy to take all channels from matteB. This should result in a perfect union of the two images. Instead I get a terrible line between them. Checking UnMult helps a little bit, but not completely.

I just don't get it. Shouldn't this be a perfect mathematical operation? Is After Effects just incapable of doing this and another compositing package will work?