InDesign CS5.5 Exporting PDF master page hyperlinks only work on first 2 pages

We recently upgraded from CS5 to CS5.5 and now our hyperlinks that go to different pages in the PDF only are working on the first 2 pages of each document in the book. We have about 30 documents wrapped up in a indesign book. On the master page we have hyperlinks that allow users to quickly go to the index in the back of the book. After the CS5.5 upgrade the hyperlinks only work the the first 2 pages of each document. We export to PDF(print) with hyperlinks enabled.
I have tried the below:
- I have tried 2 different computers
- Deleted and re-created the indesign preference file
- deleted and re-created the hyperlinks

Can you recommendd the best way to manage the following:
I'm on a Mac. Created an enewsletter for a client in Indesign CS5 with 7 "click here"s throughout the document. The hyperlinks are to connect w other PDF documents not URLs.
Where will I have the best luck creating the hyperlinks - Indesign or in the PDF I export? I have Acrobat Pro if I need to create the hyperlinks in the PDF.
Except I can't figure out how to create the links in either program as far as what name to designate and where do the PDFs reside so people can link to them? And do I enter the file name of the PDF connected to the particular "click here."

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