Strange problem after disc (folder) build CS3 - need a guru!

I have a DVD-9 project that I built over night last night (folder build)
This morning I used ImgBurn to add my ROM content and set the layer break and
burn the DL disc. Everything worked fine (as it has for the last 4 DVD-9
projects I've done)

Upon watching the DVD, I discovered an error in the last chapter on one of the
timelines. I corrected the error in my NLE, re-encoded the AVI file. Then I used
the "replace asset feature to use the new section.

I then re-built the DVD folders and the only that thing needed transcoding was
that new section, so the build went quickly.

So then I open the DVD folder in WinDVD to check everything and while I'm
flipping forward through the chapters, I notice that in the middle of one of the
timelines (NOT the timeline associated with the change I made), when I press
chapter advance, it doesn't go to the beginning of the next chapter (starts
somewhere else) and the same happens with the rest of the chapters in that
timeline. This only happens for this particular timeline and if I recall
correctly from the first DVD this morning, the spot this happening is where
ImgBurn was telling me to select the layer break position (for the first DVD
that worked fine this morning)

So thinking that the problem was with that timeline, I right clicked on its
asset and reverted it to the original so that it would transcode again. I did
another folder build, this time that was the only thing that needed transcoding
and about 45 mins later it was done.

Sadly, the same thing has happened. So after I finish posting this, I don't know
what else to do except revert all assets to original and build the folders yet
again. I should also mention, that when previewing in Encore, the chapters are
in the correct place on the timeline, same with when I select them from the menu
during preview.