I've been having a weird issue that pops up every now and again. When I import a video file sometimes the embedded audio track "stutters" a bit, repeating a short chunk (maybe three seconds or so) over and over again. The video plays fine on top of it. It's not rhythmic or consistent, just jumbled segments of audio.
Reloading doesn't fix it. Relinking/replacing doesn't fix it. Purging all caches doesn't fix it. The only way to fix it is to delete the clip and import it again, which isn't very practical when there's tons of keyframing and parenting going on.
Format doesn't seem to matter. Happens with MP4s and MOVs with all sorts of different codecs.
The two other video producers in my office have the same issue on occasion. We all have different hardware. For what it's worth, I'm using a 2013 Mac Pro running 10.9.4, 3.5ghz 6 core Xeon E5, 16GB RAM, dual FirePros. After Effects is CS6, up to date.
One possible cause is the footage itself. No fooling.
AE does NOT like compressed audio: e.g. ac3, mp3. The audio tracks of highly-compressed video like mp4's can also contain compressed audio. Audio-only clips in mp3/ac3 will also give AE occasional fits.
You can determine if this is the cause yourself: find a clip that you KNOW is going to bring you grief. Now transcode it to a Quicktime PNG file with an uncompressed audio track -- aiff is good for this. Compressor can do it, and so can QT Pro. Import it into AE, and the problem should go away.
If it doesn't help, you probably have other issues.
I don't think that's the case. One, because I know it's happened with lossless footage before, and two, because the problem isn't easily reproducible using the same clip. Sometimes the audio is jumbled, sometimes it's not, without any changes to the footage. I would think if it were a format issue it would cause some audio problems consistently rather than one out of every thirty or so imports.