This mis-alignment of Chapter Markers will often happen, when one is using any GOP structure material, like MPEG, MP4, etc. Chapter Markers can only be placed on I-Frames. This article goes into more detail on GOP structure: http://forums.adobe.com/message/2722687#2722687
If one has full I-Frame material, then Chapter Markers can be placed exactly on any Frame.
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Thanks for your speedy reply, Bill.
I think what I'll do, regarding the projects I wish to burn to DVD, is to place the Scene Markers, say, 10 or 12 frames "late" from where I would, ideally, like to have placed them, and then at least the resulting Scene Markers on the DVD will (hopefully) always occur just into the desired scene, rather than a split-second before, and so avoid the undesirable, and unprofessional-looking brief 'flash' of the previous scene which gets displayed first, when navigating directly to that scene.
If I am using GOP material, knowing that that material's I-Frames might not be 100% accurate with my desires, is to always have a Dip-to-Black Transition to about 02 sec. of Black Video, between all of my Clips. Then, I can locate my Chapter Markers on that Black Video. This also gets me that Dip-to-Black (and back from black), between Chapters. I like the aesthetics of those, and the solve any GOP issue.
Those Dip-to-Black also cover any "black flashes," that one often sees, when the DVD player's head seeks the next Chapter. The black flash will come when the screen is already black, so no one will ever see them.
I use a Dip-to-Black in editing, to show the passage of time, and perhaps the change in location (or both), and as Chapters usually feature one of those, the Dip-to-Black is ideal. Within a Chapter, if I use a Dip-to-Black (passage of time, or change in location), and the passage of time is quite long, then I will increase the Duration of the Black Video between the Clips even more. Just one way that I employ Transitions, and especially Dip-to-Black.