login via ssh to your server, find out what command your script is passing to FFMPEG, and run it yourself, see what errors come back. FFMPEG can be quite verbose, and this method will give you more info the syslog or apache logs.
my guess would be that likely there was errors in your source video, video charge is not very good at repairing things at all. you could try downloading MpegStreamClip from Squared5.com, open yourvideo file and have it repair the video file, then save it again, and restart.
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