Thanks for your bugreport.
Do you have "anacron" installed? What is the output from:
$ ls -l /var/spool/anacron/
Anacron should take care of this and it should be called automatically
on resume. Do you work a lot (mostly?) on battery maybe?
** Changed in: update-notifier (Ubuntu)
Status: New => Incomplete
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Update manager stops checking for updates in Jaunty after resume from suspend
https://bugs.launchpad.net/bugs/392603
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