A hypothetical for you..
You are connected to 2 networks, with Notify window open. It's showing, but is not the active window. Your 2nd connection drops off (for whatever reason), and reconnects. You're typing in the active window.
In 6.3 as it stands, the Notify window will grab focus, and become the active window, even though you were happily typing in a completely different newtork.
To my mind, this is annoying for secondary connections.
If the Notify window is Closed then yes, I agree it should re-open if the "Pop up notify window on connect" is checked. But once it's open, it shouldn't be a focus-hog.