Hyperlinks missing after converting Word 03 docs to PDF using Acrobat Pro 9.

I'm having an issue when I convert a Word 2003 doc using Adobe Acrobat Pro 9 to pdf that the hyperlinks are disappearing.  I've had success with this in the past but for some reason now the hyperlinks never carry over or show up in the pdf.  I also have a good amount of bookmarks making up a table of contents within my word doc that aren't making the conversion either.
I've spent a few hours thumbing through options in both the pdf printer and word as well as searching online with no luck.
Kind regards,
Tim

Alright, I've got link creation process working again.
However, now I have another technical issue with how the links are being handled.
My work has an Intranet site that these Polices and Procedures are being accessed from (http://is-intranet/policiesandprocedures/).  For some reason when you open one of these forms on our Intranet site and click one of the embedded links (that are linking to another one of the Policy and Procedure PDFs) it's adding extra text to the path. i.e. open 2.01 Employee Handbook when I click a link embedded in that form to http://is-intranet/policiesandprocedures/3.01 Technology Usage Policy it's adding an extra is-intranet to the beginning of the path http://is-intranet/is-intranet/policiesandprocedures/3.01 Technology Usage Policy causing it to not open.
I cannot seem to prevent this from happening.  Now, if I go through the form and look at the link it's correct and if re-link it to the other form everything works fine and the path of the link in the PDF doesn't change.  But now the link works correctly when opening the forms from our Intranet Site.
It's a very confusing issue.

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