I know you asked that we not post to [resolved] issues but you didn't post the resolution, so I will repost - I upgraded from 2.3.3 to 2.5.5 and now the Open and Download links result in a 404. The PDFs are stored in the media directory and the full URL is in the Publication link box.
Sample link to a publication:
The first link on this page should point to the document above.
Instead I get a 404 on all links now. Help!