When converting a word document with sections to a PDF it changes the footer page numbers from 1 of x per section to 1 of x for the whole document. For example we need the pdf to say page 1 of 13 for the first section and then page 1 of 23 for the next section instead of saying page 1 of 36 for the whole document. Excel does this also with it's sheets in workbooks. It worked like this in Acrobat 10.0, but if we patch to 10.1.3 it break this functionality.
A bug report may help, but I would also test printing your document to paper. I suspect it may be a MS OFFICE issue and you may need to update OFFICE. A while back, there was a mess of trouble with headers and footers in WORD. You may be going back that far. Generally, Acrobat creates what the application gives it and does not make such changes (but the bug report does not hurt).
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