It seems that some ad-wizard at Canonical decided that the tray icon that notifies you of available updates in Ubuntu was simply too well liked. Thus, in 9.04, they decided to make the update manager automatically pop open any time there are updates found no matter what you are doing. Luckily, for those of us that actually enjoy an unobtrusive user interface, restoring the update manager to it’s original tray icon glory is a single command away. Simply run the following and your web 1.0 auto pop-up annoyances with Update Notifier will decrease a full 100%!
gconftool -s --type bool /apps/update-notifier/auto_launch false
To make the change take effect you will need to restart the Update notifier, or log out and log back in.