Hmmm, more experimenting, I cannot repro the issue with other books. I think it was something with this one book, let me test some more and get back to you.

One other question, David. Have you considered adding something akin to what Amazon, Google Play, etc., do with their annotation systems, and attaching some kind of a 'location' integer to the note? This could be anything from a publisher's location value (I think Amazon uses this) to a a publisher's page number (which is obviously an arbitrary value based on the original typesetting).