I'm working in InDesign 4.0 but have also tried this on my laptop with v. 5.5. Most of the hyperlinks work but there are about 10 that are not activating when I save as PDF.
I have looked at your database and tried the suggestions but have still not have had success. I've deleted the preferences file 2x. I've unchecked the shared links box. I've deleted the text, retyped it in and made a new hyperlinked text. I've deleted the links and relinked them. I've double clicked on the destination name in the hyperlink dialog box and checked it or deselected the shared box.It is happening to text that is a repeated url and some that are not repeated elseware in the document.
In the hyperlinks box I've selected "go to destination" and it opens the web page in my browser. Still when I save to PDF it does not give me the finger to click on the link to the website. Please help as I'm on a deadline on this and have spent hours trying to solve it.