So is this problem solved? I'm not quite sure if you're still needing help here. If so, just re-state the question, and we'll go from there.
Some additional comments:
- You are correct, the beginning of a clip is a chapter, and there is no way to change that. That's is how the DVD-Video format works.
- There is also a limit to how many chapters can be put in a video clip, and how far apart they need to be. Software reacts differently all the time. I've found TDA to act oddly if chapter marks are closer than 3-4 minutes apart. That's honestly close enough anyway. You can put some 30 seconds to a minute apart too, but do not make it too often (else the software may crash). There is a limit of 99 chapters.
- The way to delete bookmarks in TDA is to use the toolbar on the right side of the TDA interface. It is also the best place to insert a chapter mark based on a precise second in time.
Hope this helps.