I created a test document by copying a paragraph from a Logos resource, and the footnotes came across fine. Then I built that document into a PBB and the footnote numbering is messed up. Instead of 2, 3, 4, 5, it is 12, 23, 34, 45.

(Also, note how small the font is in the new PBB book, as I noted in another thread.)
Source docx:
4744.test.docx