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Old topic, but in case anyone is still looking for an answer: If you create your custom "FileZilla Server Interface.xml" and "FileZilla Server.xml" and place them into the default folder where FileZilla Server will be installed (PRIOR to the install), running the installer afterwards with the /S command-line argument completes without any dialog pop-ups. It's a little odd having to create the install location folder instead of letting the installer do the work, but if that's what it takes..