If you've ever received a DVD and had the chapter sequencing out of order, here's how I managed to fix things by myself. One motivation is that I wanted to see if this issue could be fixed by editing the metadata within the DVD files stored within the .IFO file. I didn't want to get into the business of reauthoring the DVD and degrading the video quality.
Noticing that the chapters were correctly splicing but between Chapters 4 & Chapter 5 were not advancing, I decided to do some probing to understand why the bug was happening.. You can use a program called PGCEdit that lets you to playback/traces to see how the IFO file gets simulated in the DVD player, setting up Trace mode to walk through the sequence and watching as data in the general purpose memory registers (GPRM) and executes various commands that launch different sections of the DVD.
For whatever reason, there is an instruction (perhaps when the DVD needs to jump to the next layer) to jump back to "cell 4", the last clip that you're watching before things sequence to the next clip. I changed things to cell 5, and whala, everything works.
I then used Ubuntu ISO Editor which makes it easier to re-create ISO files from existing ones and re-burned a copy. The advantage of using ISO Editor is that you can easily add/remove files from an existing ISO file, and then generate a new one very quickly.