I have this same issue, but I think it relates to having a "user" for ssh and a separate user for ftp. Neither user can see the other users files.
If I upload files with the FTP user, then log in by ftp using my SSH user, I can't see the files the FTP user uploaded. However, I can see them if I ssh in. I made the mistake of uploading files using FTP then deleting the "FTP" user and now I can only see the files by ssh, not FTP.
Does anybody know which chmod command to use to make the files viewable by any user logged on by either ftp or ssh?