I actually had the exact same problem – I just upgraded to 2.5.7.2 from 2.3.3 – and all of my links for the publications got updated to the new permalink structure. Clicking on either download or open resulted in a 404 error. I was able to downgrade successfully however by deleting the plugin and uploading the previous version with no issue.
Unfortunately I don’t have access to logs (unless you know where logs are kept on godaddy) – I’d be happy to pass them onto if you like and I can find them
