Web browsers like Firefox, Google Chrome use there own PDF viewer so links might now work.
Have you tried opening the PDF in Internet Explorer?
Are the hyperlinks working perfectly in Reader/Acrobat?
I'm talking about opening hyperlinks in PDFs opened by the Acrobat application, not in browsers.
I'm trying to get Acrobat to open the links in PDF files in my browser; instead Acrobat downloads the linked webpage and converts it into a PDF and doesn't even call the browser.