In the new version, if you have the "pop up notify window on connect" option enabled this will force the notify window to take focus every time you connect to a server, even if the notify window is open. I had to make this change because of other issues. When you disconnect from all servers, the notify window is automatically closed.
I can change this in the next version so that 1) the notify window only takes focus the first time it is popped up and 2) the notify window is not automatically closed when you disconnect from a server. This should ensure that it remains unobtrusive most of the time.
How does that sound?
