I have resolved this issue, so I wanted to share in case it might help someone else now or in the future. The Blu Ray disc I was burning had two video clips (with corresponding audio) - a wedding highlight film which was 3:31 and a wedding feature film which was 1:27:30 in length. For some reason, placing both of these films on the same timeline was resulting in the audio being "chopped off" at the end of the second chapter (the feature film) leaving 3:31 of no sound - exactly the length of the highlight film (chapter 1).
So instead of making each film a chapter on the disc, I put each one in it's own timeline, relinked the menu buttons to the clips and it works perfectly. I don't know why it should matter, but in this case, it did. So 14 Blu Ray discs later, it's fixed.
I also wanted to thank the awesome Adobe forums community, and especially Stan Jones, for all the help you provide to not only myself, but the entire Adobe user community.