I manage a server for a client that has the FileZilla Server running as a service. Every time I connect to the server and login the FileZilla Server Interface loads and pops into focus which after some time gets a bit annoying since it is rarely needed. It appears that the option to load the interface is set during the installation procedures and there is no obvious way to disable it post install.
I did however come across a little gem in the registry that can sort the issue. All you need to do is navigate to the following key in the registry:
and remove the "FileZilla Server Interface" entry and the problem goes away!