Nina found the issue! She sent me this (I trust it's ok with her to quote):
"It appears there was an issue with internal links in PDF files generated from Word, and Microsoft issued a patch for the Windows version; however, it’s not yet working on Mac according to the latest replies in that thread, which are dated October 27 at this writing."
It turns out I was wrong that the pdf links work the in un-uploaded document. They don't. :-) So this is just the Mac bug.
Messages are the sole opinion of the author, especially the fishy ones.