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That is my problem, too. Almost every MPEG stream (e.g.
digital TV recordings) has some errors and that causes mm2d
not only to change the lengths of the stream but also
results in pop-up panels that have to be clicked away by the
user. This means I have to sit next to my Mac for hours
simply to say "ok" to a few windows and the converted
Quicktime result is no longer in sync with the audio track. :-(

I would be willing to invest some time in this ... why is
the source for the latest release not available for download?

Matthias