Depending on the security mode and FTP mode, you may need to adjust the permissions on these files and folders to permit access through FTP. In Share mode or Anonymous FTP mode, the NAS will see an FTP user as a user named "ftp". Therefore, files and folders will need to be accessible by this user for them to be accessible via FTP.
The easiest way to allow access to a file or folder is to go into Windows, right click on the file and select Properties, then select the Security tab, and add the required permissions to the "Everyone" setting.
In User-based FTP mode (available in User and Domain security modes), the ioSafe R4 NAS will see the ftp user as whichever user's credentials you used to login. Therefore, if you logged in as user "ewok", the ioSafe R4 NAS will see you as "ewok" and will allow you to access files and folders that are accessible by "ewok" when mounting the share in Windows.