Chapters can only be created at I-Frames (roughly every half second), but I don't guess that's your problem. While VobBlanker can do it, as you discovered it may be difficult to choose the chapter points accurately. That's why I also said in my post that I'd do it a different way involving demuxing, creating chapters, remuxing, and then sticking the new DVD with chapters back into the old one that didn't have chapters, thus getting back the menus and anything else that might have been in the DVD. Doing it that way allows you to be as accurate as that I-Frame requirement allows.
Any authoring program can create chapters, but I believe that VobBlanker is the only program that can do it without first dismantling the DVD. Even those authoring programs that accept VOB input will still demux them internally.
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I eventually ended up with playing the DVD files in PowerDVD and wrote down the timestamp minutes and seconds where I thought there should be a chapter.
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That's pretty much a recipe for getting them set at the wrong place since PowerDVD uses non-drop frame timings. That is, it calculates times at 30fps while the film is playing at 29.97fps. So the times as given by PowerDVD will be before the real time, how much ahead depending on your place in the movie, but a little over 3 seconds per hour. This assumes you're in NTSC land. Maybe you discovered the problem. If you're in PAL land, ignore this paragraph.
Maybe someone else has a better solution.