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Make sure the sample rate is the same in the footage, project settings and render queue.
I can locate the sample rate in the AE comp, but cannot locate it in the footage or render queue. Where do I find the sample rate?
Load footage with audio into project window. It should list what the sample rate of that footage is, typically 48khz. Take a look at File/Project Settings. Audio Settings/Sample Rate should match the footage. Lastly, in Render Queue, in Output Module, you can specify the sample rate under Audio Output. I think that defaults to 44.1khz and that might be your problem. Try changing to 48khz.
You can get info about the sample rates by simply selecting the footage in the project panel. just like the video specific stuff like resolution and color depth, sample rate will be displayed in the info pane at the top. if it isn't, then you are using a source file with variable bitrate and/or a multiplexing pattern AE does not understand, such as some MP3 variations or embedded audio in some MPEG-4 files. This would quite nicely explain any issues on the rendered output and in such cases the only resolution to the problem is to convert the files into a WAV/ AIFF before using it in AE. For the output, simply follow David's guidelines. Be aware, though, that clean audio playback is also affected by your system settings, so double-check your audio hardware settings and make sure the sample rates are not set to exotic and unnecessarily high values or you are not using any "enhgancement" functions. In theory today's computers have enough performance to do thjis all in realtime on the fly, but you never know...