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There's a philosophical difference between delivery codecs (e.g. mpeg4, avchd), editing codecs (e.g. DNxHD, ProRes, Cineform), and capture codecs (e.g. r3d, DVCPROHD). While almost any codec can be used for each of these three stages, your workflow needs will help you decide which are best suited for each stage. The question you seem to be asking, is ...

My guess would be that AfterEffects is assuming something about the audio format which Quicktime is handling correctly but AE is not. Check your format settings; you might need to specify a different byte ordering (also called "byte swapping") or tell it to be explicitly 16-bit instead of, say, 24-bit. In Quicktime you can see what the audio format is via ...

I've never encountered this problem, so unfortunately I can't give you advice on how to fix it. However, next time, I would suggest that you convert all your footage to the same format before you begin editing. Prores 422 is a great editing codec. Go to this website and download MPEG Streamclip. It's a free program that converts your footage to different ...