I've had that happen before myself, and I believe it's because DVD-A does something to corrupt or loses track of the small file created corresponding to chapter marks(I believe it's the file with the 'sfl' extension). Try deleting that file and go back to your movie clip in DVD-A and click on the icon for saving the markers to create a new one. If that doesn't work, try deleting the file and changing the position of a marker or two just a bit and then re-saving the marker file. I don't know if this is the problem in your case, but it worked for me. I had to sequentially delete the assets in the project until I could get DVD-A to do a trial build. I then reimported the 'problem' assets to see what wasn't working. I decided to start a new project with the problem asset and found that the movie file that didn't work with the old project, would with the new--so something other than the asset itself was the problem. Turned out it was the marker file, and correcting that fixed my problem.

Jim