MP4 Conversion Issues

I have been converting all of my avi files to mp4 files.  For the most part, everything has been going well, but I have been running into issues from time to time.  I see sporadic errors in the ffmpeg output about not being able to render a frame.  When I play that movie using the MK802 bundled HD player, I run into an issue.  Part way through the video, I hear a pop, the video freezes for a fraction of a second, then the audio sync is off about 1/2 a second.  The pop does not cause the file itself to have audio sync issues.  If you rewind then immediately fast forward, you get right back where you are and the audio sync is fine.  This tells me there is an artifact in that point of the file that causes the video player to mess up.  I haven't tried playing the mp4 files in MX Player or Mplayer (on Linux) yet, so I don't know if it occurs in all players or just the bundled HD player.