This is just a swag, but it probably means the markers are not frame accurate. If you go to the customize section on the render template and select "place I-frames at markers" you will get frame accurate chapter marks.
Scott,
I don't think so. I did the "place I-frames at markers" when I encoded it from V7. I did get them to go away by deleting the marker that I had inserted at the beginning of the video and re-encoding. DVDA seems to want to put a default marker at the beginning of the video when it is pulled in and got confused when there were 2 there - the one it put in and the one I put in. I did get a warning that 2 chapter points were within 1 second of each other tho.