Some of the items in the listing have been marked as 'hidden' by the server administrator, and CyberDuck is using a special command to force those items to be shown in the listing. Yummy FTP has an option to use this special command, but it is disabled by default for compatibility because many servers do not support it.
To enable the special command, select Preferences from the Yummy FTP menu, then enable the 'Issue LIST -la command' checkbox and click the Save button to apply the change.