Still having this issue - Adobe Reader has added the same %0D code at the end of every URL link. I've googled and learned the code is ascii for either a carriage return or a space. Why would Reader or Acrobat add code that isn't in the URL hyperlink in the first place?
I personally use PDF-XChange Viewer and it has no problem with the links.
Why don't Adobe's own programs work with each other?? This is TOO frustrating for words.
So far, so good. The script mentioned in the link above did indeed solve the problem. Still no idea how the carriage returns got in there, though. But in our case the links were copied from Word so perhaps it's an issue interacting with MS Office products.