Page numbers wrong in PDF - original Quark file ok!

We do magazines mainly and have a Homes and Interiors publication which I have produced for over 7 years. The workflow has changed over the years and is now a PDF one as you'd expect. We output from Quark 7.31 to a postscript file then distill using our custom job option file as provided by the printers we use. Then the files are uploaded to the Agfa Delano system for them to process.
I just had a call from them to say some of the page numbers were wrong so they removed them. The page numbers are inserted using the auto numbering in QuarkXpress and the original file is correct.
The odd thing here is it's not that pages are mixed up - it's just the page numbers that are wrong - the content of each page is correct!! The only change we have done recently is go to Acrobat 9 which obviously uses the new Distiller too - but I am still using my Acrobat 7 printer option when I go to the Print dialogue within Quark. The magazine is 128 pages if that has any bearing and the pages with wrong numbers on them are in sequence (92-111).
Has anyone seen this kind of thing before or are there any known issues with Distiller 9 that could cause this?

Why don't you export the pdf from Quark using the latest pdf printer available?

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================================
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