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Well, what are the actual source files for the audio? Sounds like you are using MP3 or embedded audio in compressed movie formats, which is pretty no-no when it comes to AE. Also, AE does only linear resampling and mixing, so you may inadvertently exceed levels here and there. You should by all means make sure your sources are clean to begin with, meaning they should be 44 kHz/ 48 kHz WAV files, properly normalised. Aside from that, you can always find audio mixing tools either as trial versions (Audition, Soundbooth, Cubase) or even free (Audacity), several of which allow you to import reference video files to achieve sync. Also consider VirtualDub and similar tools to fuse your audio mix with the video.
The versions prior to CS3 had some definite sound bugs that could cause pops (and worse) especially when using MP3s. Sound support in CS3 and CS4 is much better.
- Jonas Hummelstrand
Actually I'm using MP3 44.1 kHz. Thanks for advice, I will check if converting it should help.
Edit: It really works! So the solution is to using WAV instead of MP3. Big thanks.