Pending update notification is not cleared, when the new update is installed by manually by using non AutoUpdate method. For eg
1. user has 6U1 installed
2. user is notified of 6U3 update, but ignores it
3. Then install 6U3 manully by visiting java.com or using online or offline installer.
4. logoff & login
5. The user is shown the pending update, which is not relevant anymore.