Matthew Brunn said:
“Chapter marks can only be output from the timeline!”
I would like to expand on Matthew’s very correct statement. A very common problem with people putting in markers in their output is they put markers on clips instead on on the timeline. A marker on a clip shows up as a pink marker on the clip in the video track, whereas a timeline (or sequence marker) shows up as a green marker in the timecode area above the set of V tracks. No clip markers are exported when you export this sequence, only sequence markers are exported. When adding markers to your sequence, ensure that no clip is selected first, to ensure the markers go on the sequence and not the clip.
After you’ve exported the QuickTime reference movie from FCP, open it in QuickTime Player Pro and extract the text track and export this as a text track. you can then open this is TextEdit to see the chapter markers if they are there.
Bill Lee