I cut advertisements out of my (MPEG-2 encoded) TV recordings with MPEG2VCR (now called MPEG Video Wizard; see
http://www.womble.com ). Perhaps, it can help with your problem, too: open the source movie and simply save it (hotkey: Z) as MPEG-2 Transport Stream (I think this is the stream type that has timing information embedded, to help with keeping sync between video and audio and with seeking inside the stream easily). Good luck!
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Joe Forster/STA
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