ioFTPD is a background/server process. ioGUI is just a front-end and thus a useful way to interact with the server but closing it has no effect on the server itself. From the ioGUI console (or any FTP client) you can type "site shutdown" for a timed graceful shutdown, or force it via "site shutdown now". Those are the preferred methods for shutting the server down. Killing it via the task manager isn't suggested so long as the server hasn't locked up.
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