Have you ever wondered why a package pinned with, say, synaptic after a couple of days is listed to be updated when using apt-get update? There is a bug persisting at launchpad for the synaptic package. As Michael Vogt, lead developer of the apt family, suggests an easy workaround is to symlink /etc/apt/preferences to /var/lib/synaptic/preferences or vis versa. Also, the issue that when you select a package from the list to be pinned (Package -> Lock Version) the list will be emptied. After you research for that very package it will show a lock next to it (in the state column).
Pinning a (deb)Package systemwide for apt-get and synaptic alike
Sunday, 9th Sep 2007 at 18:19 (technical stuff)