On our company intranet site we have procedure manuals. In several there are hyperlinks that point to files on the same server hosting the intranet. When we edit a Word document and then save it as a PDF using Adobe Acrobat 9.4.0, it seems to skew the hyperlink. For example, if our IIS website is called BANK and the server is called SERVER the link looks like this after the conversion:
I know it may not be the answer you are looking for but it works for me.