I've exported an animation from Cinema 4d using multipass for import into AE. Here's the setup for my multi-pass render:
When I open the aec file in after effects, the layers seem to come in as they should. I switched my color space in after effects to linear, to match my c4d output settings. I'm not bothering with any of the lights or cameras from the output--I just want to composite a background into the animation in After Effects. However, my specular, refl, refrac, atmos, and shadow layers all are rendering a black background--even when I have the blending mode switched to Add or Multiply.
I'm pulling my hair out, I'm sure there is a simple setting I'm missing but I can't figure it out. I've opened these layers in photoshop and they seem to render with transparency as they should--however, the black is rendering black in after effects--even when it's blend mode is set to add. Here's a screengrab of my composition, with the specular layer soloed, in add mode, rendering black on top of what should be a checkerboard:
Another thing to take a look at is how your alpha is being interpreted in after effects. The bright spots at the edges of your objects look like an improper interpretation.
I'll also add that the best way to do a multipass composite in AE is to blend all of the unpremultiplied layers with full alpha (e.g. Since you're using a straight alpha you could set Alpha to Full On in the shift channels effect) and then apply the alpha to that composite. I often use a layer at the top of the composite with the stencil alpha blend mode to do that.
If you blend all the layers together with their alphas enabled you'll end up with incorrect rgb values along the edges of the alpha.