Alice, I've figured out that there is an issue with when the PDF is created, for some reason the website or email address is getting segmented, thus not recognizing it as a FULL web address or email address. I opened the PDF in Illustrator to examine it and the web addresses and email address were being looked at separate words connected together, so they looked right onscreen, however, they are not being recognized as full links because of this segmentation.
Here is possible solution, which I believe works. Let me know if it does and mark my response as helpful
Save as Web page (.htm, .html) first, then save as PDF. I believe this fixes it.
schonk