I've noticed with a lot of files that now have nice chapters that Perian recognizes and loads them into Quicktime players and they work great. I did find a way to move the chapter data from the original file to the converted one but it was just an experiment and much too difficult to add to my current workflow. It would be fantastic if TranscoderRedux could preserve special data like chapters through a conversion to iPhone formats because it is able to utilize chapters I've found. Thanks guys!
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