Inter-book links not working files generated with Acrobat 9 Pro

Dear All,
We're using TCS 2.5 and generating PDF using Acrobat Pro Extended 9 from our FM 9 guides. We have many links between guides and these links no longer work. Now only the xrefs within a guide work.
We have the same relative paths for the FM guides and PDF and keep all the guides open when generating them and when generating the PDFs.
The links appear active (acrobat displays the little hand) but when you click the link nothing happens.
We have no problems using FM 9 with Distiller 7, but we've upgraded to TCS on some machines and this is where we're having this problem (on machines with Acrobat Pro Extended 9). Does anyone know if this is a bug? or a conversion setting that we don't know about?
Thank you for any help or suggestions you can provide!
Regards,
Susanne

I've found that down loading the PDF file to the Nook and using Acrobat  reader allows the links to work, however this is way cumbersome, any way to work on files directly on Acorbat.com?

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