I have been spending a few days taking old flash files, putting them into After Effects and creating .Mov files. They need to go through AE to do this as I am also creating new composition sizes.
All of the videos have worked without problem, but I have one - when I drag and drop it into the composition, and render it etc - the audio seems to start from half way through, even though the video is starting from the beginning.
was codec are you using for this file ? (and what version of AE ?)
If you can play your file correctly in a media player, then i'll go thinking that AE have trouble to read it.
Try exporting only the audio in WAV and then reimport the was put it in your composition, a deactivate the audio from your movie layer.
On the wav file, press LL to reveal the audio waves to be shure it start at the beginning of your viden, and then try to render your movie again.