I am getting an error on page numbers for a book file when I export to PDF. The page numbers are set in the master pages and when I export each chapter individually the page number show fine. When I export the entire book, then some of the page numbers repeat. The pages are the right pages, but the numbers change incorrectly. For instance, the sequence goes, 58, 59, 58, 61 and 72, 73, 72, 73, 76.
I've updated to the latest InDesign (7.5.2) and have tried multiple PDF export options (High Print, Press, PDF/X, etc) and nothing fixes it.
This is a known (and fairly catastrophic) problem in CS5.5.
Some people have found exporting the individual INDD files to IDML, resaving them as INDD files (don't overwrite your originals!! Make a backup first!), and recreating the book works...for a while.
You could revert to CS5.0 if you have a license for it.
CS6 is on the horizon and should fix this bug.
Hopefully there'll be a CS5.5 maintenance update to do so as well.
Sorry I don't have a better suggestion.