CyberDuck always causes a Leopard firewall warning: "Do you wish to allow incoming connections..." It doesn't matter if you click Allow or Deny, they still happen once each launch, when you first access an FTP server. This happens even though I added CyberDuck to the System Preferences firewall app list (with Allow, not Block).
It may be that this only occurs if you are not an Admin user. (I don't run as admin, for extra security, so I haven't tested that way.)
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Still occurs when running as Administrator. This is because the Leopard firewall is no longer port-based, but uses code-signing instead. I can't find the article at the moment, but there's something in the developer documentation that tells you how to fix this.