I'm aware of the missing verse reference problem, and at first I thought this might be related, but there is nothing special about the word that is missing from my compiled book. The word is "Princeton" and it is normal text like the text before and after it.
Source Microsoft Word document:

Resulting PBB book:

The word is just gone. Does the PBB have something against Princeton? [:P]
Here's the source file: 3660.Infant-Baptism-Scriptural-and-Reasonable.docx
FYI: I'm saving as docx from MSWord 2003.