InDesign won't print all files in "Book" to PDF

I have 69 .indd files created in CS5 (ver7) that are part of a "book". I have been trying to "print" this book to PDF so I can submit a single PDF to the commercial printer. I do this all the time and have never had problems like this, but this is a new publication.
Here is what happens: I select all the files defined in the book, then click on the "Print the book" icon. After InDesign gathers all the document information, I select my Print Preset, with "Adobe PDF" as the printer, then print. After processing a few moments, I save the file, and InDesign/Acrobat starts processing the PDF. The complete book is 542 pages, but the PDF file pops up as completed with only about 38 pages processed; in the meantime, InDesign/Acrobat is still processing the files, but results in no new PDF file created.
I have rebooted and the problem has persisted.
In addition to this, another problem has cropped up and I wonder if it is somehow related. Parts of a master page (page heading) mysteriously appear on a page defined by another master page. There is no way to delete this unwanted heading, even if I "Override All Master Page Items".
Any help is appreciated.

I would recommend exporting the book to PDF rather than printing to PDF....
Master objects from a different master might be appearing if they are on the other half of a master spread that is applied to the other half of the document spread and they touch that side of the master as well as being on the half not in use. Check the master in questina and be sure that the objec is not crossing the gutter.

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