I had this message, and since I did not find a solution on internet, I decided to share my experience.
I shrink DVD9s to DVD5s with DGIndex->CCE, VOBEdit->IfoEdit and Vobblanker.
This way I can reencode and replace audios to reduce the size.
This time I also replace DTS sound with some 5.1 Ac3 language stream which was not present on original.
When authoring DVD with IfoEdit with 6 audio and 6 subtitle streams after some 25% IfoEdit gave messages like data arrive too late, and after some number of these messages stopped saying: Too many lost frames.
I tried to author these files also in Scenarist, but I stopped because it seemed to me a task too huge to import all subtitles.
I set a DVD Reauthor 1.5 Light to disassemble assets for Scenarist. It prepared me a quite unhandlable Scenarist project which had at least almost Scenarist ready subtitles. (I say almost because they all were split in 5 parts and timecode started with 1 hour and they had references to blank bitmaps with custom color and brightness settings which I removed.)
Finally I found out that subtitles are making all trouble, because Ifoedit also said, data will arrive too late in stream 20 which is first subtitle stream then in E0 which is video.
The easiest way to encode back to sup for me seemed a creating of slideshow in Scenarist with one 3 hour dummy slide and all subtitles, then demux with VobBlanker.
When I used new reencoded subttitles IfoEdit did not complain almost at all.
Although the file sizes of new streams were similar to original.
I assume that these problems were part of kind of some new "copy protection" - a corrupted parts of DVD with links to walkaround them on players, but to trap into when ripping.
Probably there is more convenient way to cure such sups.