there are many reasons it could be jerky. the most obvious would be that the file resolution or bitrate is to strenuous for your hardware. What is the file size, movie length, width and height of your movie? What speed is your processor, how much ram, what versions of OS X and QT do you have? Also if you happen to be playing the movie on a second video card or something, try the main card (high res videos play choppy for me on my PCI radeon card but not on my AGP card).
The next most obvious reason might be a software conflict or bug. What are all the files (and version numbers) you have in /Library/QuickTime and ~/Library/QuickTime? To elaborate, I don't know what might cause a problem, but I can tell you what if anything you can remove to see if the situation improves. Further, you need DivX to play divx.avi files with mp3 audio, and you need the xvid delegate to for it to agree to do the same for xvid.avi. 3ivx is a faster decoder than divx, but each has their own separate bugs, especially on xvid stuff, so if one doesn't work, try the other (the only real way to do this is by removing the 3ivx codec, which will override other mpeg-4 decoders). You want the latest versions of everything too.
I suppose it's possible the text track is causing problems, but I would rate that in the less than 1% category of likeliness. If the file plays the same when you just open it in QT without adding chapters, then obviously the chapters are not the source of the problem.
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