One thing I've noticed is that sometimes spaces or foreign characters in audio files causes issues. Here's my (as far as I know current) list of bugs that I've encountered with iBooks, some of which relate to audio problems:
This page has info on avoiding special characters or spaces in both the Widget Name and the names of files in the widget:
Are you able to share a portion of a your Hype document?
Do you see a difference when previewing in iBooks for Mac?