I am also seeing this issue in Lucid Lynx (Alpha 3) in a Virtual Box VM.

Could it be significant that my update system is:

aptitude update
aptitude -d -y dist-upgrade

Then run update-manager via the GUI to actually install the packages
that the command lines above?

Perhaps aptitude is not setting the flag because it did not actually
install anything.

-- 
thinks that package information is 8 days old even after updating an hour ago 
(aptitude does not write update-stamp)
https://bugs.launchpad.net/bugs/454941
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