I can’t think of anything that might be causing it to happen (not that there is not a cause for it).
You can do some of this with timelines, but if it must have subtitles, it’s going to be a lot of work (each subtitle will have to be typed in manually). There’s no manual advance on timelines, so you’d have to lose that as well if you decide to go that route.
Is the need for subtitles more important than getting an otherwise working DVD out as soon as possible? Sounds as if that’s a question you need to consider.