I'm assuming he installed a modified hildon-desktop,
didn't you?

apt-get update shows the original desktop as the update to the modified hildon-desktop, but crapmanager shows the small hildon-desktop update (which isn't a real update if your using a modified hildon-desktop of course) as a whole Maemo 5 update, but that only includes the original hildon-desktop as the N900 thinks that your running an outdated one.