In Ubuntu 9.04 (Jaunty), the new default behavior of the update-manager window is to pop up minimized when critical security updates are available. This differs from the previous behavior of adding a notification tray icon when any type of update is available. This is presumably to nag users to apply critical security updates, similar to something Microsoft did in XP a few years ago.
I personally think this is a very bad decision because it is annoying and also assumes that Ubuntu users are too lazy to apply their updates promptly. In any case, as documented in the Ubuntu 9.04 Release Notes, here is how you fix it.
gconftool -s --type bool /apps/update-notifier/auto_launch false
