This change is documented in the release notes for Ubuntu 9.10:
http://www.ubuntu.com/getubuntu/releasenotes/910#Change%20in%20notifications%20of%20available%20updates
Directions for restoring the previous behaviour are also provided there.
** Changed in: update-manager (Ubuntu)
Status: New => Invalid
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Update manager shows its window every time it finds an update
https://bugs.launchpad.net/bugs/488356
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