I've asked about something like this before, but I've found a new issue...

A friend of mine captured an episode of MST3K, complete with commercials on his standalone Phillips DVD burner. He eventually figured out how to re-author the DVD+R to remove the commercials, such that the DVD will play without the commercials, BUT... it has been my intention to re-author what he captured on another DVD, with menus, etc. I was able to use DVD Decryptor to rip and demux the VOBs to m2v and ac3 streams, and then use those files to author a new DVD using Encore. I did a quick burn, without building menus, etc. and it played ok. Then, I went back to insert chapters, create motion menus (via video buttons), etc. and found several oddities that seemed to be related to/caused by the MPEG-2 stream itself. First, when assembled in a timeline, the m2v and the ac3 file are not in synch, even though they ARE in synch when the DVD is authored. Secondly, in stepping through the timeline to place chapter points, the preview window won't update correctly, as I try and place (for at least the first 30 mins. of the video) the chapter points. Thirdly, once I get most of the points place (mostly incorrectly), I go to the "Chapter Select" page to place the videos buttons for the chapter points, and THEY don't update correctly (and don't reflect the proper point in the film). Then, once all of this is authored, the movie itself plays fine, but the motion menus on the chapter select page don't move correctly AND, if you jump forward (or backward) to the next chapter point, the disc plays for a couple of seconds and FREEZES. It will still go backwards or forwards, chapter-wise, but unless you go back to the main menu, the disc won't play at all.

Has anyone else experienced these problems, and/or does anyone have any suggestions as to how to fix these issues? I've considered using ReStream, but truthfully, I'm not sure what elements of the MPEG-2 stream I want to add or remove.

Thanks for whatever help you can offer!