Some files/directories are not listed by ProFTPD server

With ProFTPD server there are many configuration directives that can cause the server to hide certain directories from a client, including:

• HideFiles – Enable hiding of files based on regular expressions
• HideUser – Enable hiding of files based on user owner
• HideNoAccess – Block the listing of directory entries to which the user has no access permissions
• DenyAll – Deny all clients
• DenyUser – User based deny rules
• DenyGroup – Group based deny rules
• DenyClass – Class based deny rules
• Deny – Access control directive

You should be able to see in ProFTPD log file why the server hides the files.

Check /etc/proftpd/proftpd.conf and other ProFTPD configuration files, including virtual host-specific configuration files. Look also for any .ftpaccess in the directory and parent directories.