Hi,
If you pull the VOD file using RTMP, then you will likely see problems. RTMP is very bursty when being generated from a vod file. There are two things you can do:
1) Use RTSP to pull the vod file instead (this probably won’t solve your missing data at the front of the file)
2) Use our HLSCreator application, which converts a file to an HLS playlist.
Send me an email or IM if you want to try the HLSCreator.