I experienced the same problem with 4.4.1 but it seemed to resolve itself after I futzed around with the directories for almost a full day.  I saw a post about foreign language characters and the only thing I had close was a folder with a name all in caps.  I removed that via FTP, added and deleted new folders via the file manager, resynced multiple times  Also did everything over with the Auto-sync setting in the host setup on and off.and it eventually resolved., but I am nt sure what did it.  Now, however, I download any file from my site through the file manager or link to files on my site with the link manager. or any module that seems to use link.aspx. (Repository, etc)    Still do not know what the problem is with that.