Same problem here. It seems to be a bug in apt-check:
| % /usr/lib/update-notifier/apt-check
| Reading package lists... Done
| Building dependency tree
| Reading state information... Done
| 11
|
| # aptitude dist-upgrade -s
| Reading package lists... Done
| Building dependency tree
Package: update-notifier
Version: 0.42.12-3
After updating the system using the update-notifier, the main window
shows, that there are no more updates available. In contrast the
tray-icon still shows the number of updates available before using the
update-notifier.
I'm using Debian testing, kern
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