When I render out an audio only .AIFF or .WAV from After Effects, Cinema 4D won't recognize it as valid. I have to re-export the audio file through Quicktime Player or iTunes. Then they work fine.
So is AE not writing something into the audio files that C4D is looking for?
Why am I not surprised? C4D seems pretty messed up these days.... Anyway, rather than AE not doing its thing I suspect C4D chokes on additional data in the files which could be markers or XMP metadata, so make sure to turn these features of when rendering.