This could happen if audio/video is received after the first fragment has been created. To ensure this doesn't happen audio and video should start at the same time.
What I suggest is that you clear out the streams folder under livepkgr and the .stream file from under livepkgr/events/_definst_/liveevent, restart your server and then start your audio-video publish at the same time. Are you using FMLE to publish the stream?
If that doesn't help, you can try increasing the fragment duration in the Event.xml.
Let me know if that works.