In general, I like the way it's working now.
My own suggestion would be:
- if "pop up notify window on connect" is checked: refocus on (every) connect, close on disconnect : a "who's online" for the "messenger generation"
- additional check for this option: "...open minimized" (and maybe: "...hide in treebar/switchbar")
- if "pop up notify window on connect" is unchecked: no open/focus/close/show/hide on connection-events: the notify window will only be called manually or via script.
EDIT ...then again, that's many additional cboxes ... your idea is conclusive