How to keep chapter markers in H.264?

I have some long videos (1 hour) that I have output using FEC to Quicktime Movie. These videos include several chapter markers placed in the timeline. The video plays back fine in Quicktime Pro and I have the drop down menu of chapter markers... but the file size is huge (12 GB). I can burn these to DVD and the chapter markers are included.
However, when I then compress (using Compressor 2.0.1) to H.264 800 Kbps (reducing the file size from 12 GB to 300 MB, etc. )... I lose the chapter markers altogether. The video plays fine but the chapter markers are gone. I'd like to keep the compressed videos on my PowerBook at the smaller file size ... play them back using QuickTime Pro. But I lose the markers. Any way to keep these markers in the conversion process?
Thanks.
Jeff
Message was edited by: Jeff Morgan1
jmspeaks

Have you tried the option to Add to Selection & Scale instead of Add to Movie?
In case you haven't seen it yet, I believe this tutorial on QuickTime chapters is basically what you'd like to do. I think Step 8 and on is what's relevant to your situation, though instead of opening up a text file, you've got an extracted track.
Let us know how it goes.

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