In poking around, I discovered that the reference movie files that iMovie2 and iMovie3 create can be read by Quicktime Player. iMovie3 projects will also contain a chapter track for iDVD chapters that Quicktime can also detect. So to fix the sound of an iMovie3 project while also keeping the chapters, I figured I'd try to copy the sound track from a 'good' project and paste it onto the 'bad' iMovie3 reference movie; luckily, it worked. Here is how I proceeded (it requires QT Pro):
- Using iMovie2, make your project as usual. Note that it might be possible to edit everything in iM3, load it up into iM2 to fix the sound, then go from there; I do not know if iM3 specific effects will get loaded into iM2, however.
- Save the movie, then export it as a large full quality movie file from iM2. We'll call this backup project "B."
- Load up your main project in iMovie3; at this point, your transition sounds will become corrupt. Add your chapters and save your project.
- Load up the main project in QT Pro using the reference file (available in the root of the project's folder); delete all sound tracks by using the Delete Track... item in the Edit menu.
- Load up project "B" in QT Pro; extract the sound track. Copy it into the clipboard.
- Go back to your main project in QT Pro, select Add... in the Edit menu (make sure the playhead is at the start); the new 'good' sound is now part of the main project, while still keeping the chapter markers. Save the project.
- Load iDVD3, import the reference file, and you're good to go.

