Sorry, I should clarify... what are you comparing update-notifier's info to?
It will not match what synaptic reports because it is only able to compare package lists from one update check to the next; synaptic uses a different algorithm.. I'm not sure what it is, but it seems to be based on a longer time frame.
Update-notifier's calculation is also user specific; update-notifier is run with current user permissions. Its' logs are stored in the home directory of the user that is running it and are unique to that user. This means that if one user runs update-notifier then doesn't log in for a period of weeks and a different user that has run it more recently, the "new" package list they see if they log-in and run update-notifier at a similar time will be different (although available updates should be the same).