[FFmpeg-user] Frame Drops and Audio Sync Issues

[James Board]

I captured some video from a hardware capture card.  It has a few hundred frame drops in one hour of video.  The container format is .avi.   When I play the captured file with mplayer, the audio is out of sync with the video.  The same is true if I encode the video with ffmpeg and play it with mplayer.
Is there any way to use ffmpeg to sync the audio with the video?  I know it's possible to extract the audio from the avi file and stretch/compress it to match the length of the video.  I'm not talking about that.  I'm wondering if timestamps are typically stored for both audio and video and if there is a way to somehow modify the avi file so when I play it, the audio is in sync with the video.