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Asked this question before... having same problem.

When I go to the RAM preview of After Effects, the audio of the video will play on sync for a while, then will get screwy. Sometimes the audio will jump ahead or before it should. It is making the sound choppy and my characters sound stupid.

Please, I need a solution!

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up vote 1 down vote accepted

Sounds like After Effects is having a problems reading the audio from the file. I'd suggest converting the audio to a separate .wav or .mp3 and importing it back into After Effects:

  1. Open Adobe Media Encoder
  2. Drag the file in question into the que
  3. Under Format select Waveform Audio File
  4. Leave the preset at its default
  5. Click on the yellow text under the Output File column to set the new files destination
  6. Click the Triangle to begin encoding

Then use this new file in After Effects and it should work fine.

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How would I go about doing this? – parion May 11 '12 at 3:17
@parioscreations I've added to my answer :) – OrangeBox May 11 '12 at 5:35
Great answer! But how do I select Waveform Audio File? I only see MP3. – parion May 26 '12 at 20:43
I always forget which codecs are default and which I installed myself. To be able to export WAV (Waveform Audio Files) you will need Flip4Mac. But you dont have to use WAV. You could just export it as a MP3 which would work just a well – OrangeBox May 28 '12 at 1:03

Try to convert your video into ProRes422. I guess the video codec of your source material is using some sort of compression, that After Effects is having problems with and is loosing sync.

On OSX ProRes422 comes with Quicktime or can be downloaded as a free Update for Quicktime. But if you only have a Win7 computer to work with, you can use FFMPEG: it supports ProRes422.

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