When I worked with R11, I never had a problem with External Compositing tags. They always came in perfect inside AE.
Now in R13 the biggest issue is that the null or solid the EC tag creates drifts from where it should be. And a smaller issue, my null or solid from C4D is always rotated 90 degrees. I'm applying the EC tag to a polygonal plane object (with no depth). I don't see why this is happening.
But the biggest issue is that it drifts and doesn't line up well at all. It seems to be off in Z space or something.
Never mind I came across the answer. For those suffering from a similar issue, what worked for me was to position my plane at a +Z orientation in the primitives parameter then rotate it to it's necessary angle after that. Sounds like a bug because I should be able to compensate for any rotation misalignment inside AE, but apparently not.