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.