I have yet another theory about the dreaded chapter markers that have caused problems....
Should you have the interest and have QuickTime Pro, open one of the original files with Chapter Markers that has been causing grief.
- do a Command J (show attributes), you will see four tracks
- select the Text track (the chapters) and Uncheck the little checkbox toward the bottom of the window that says 'Cache'
- Save the movie.
- Quit QuickTime Player and then try the file again to see if it works better.
Somehow this little checkbox (which is certainly not needed for regular playback) has become checked and I have a sneaking suspicion about its role in the playability of longer files with more markers