I assume you have "delete tracks that aren't on the auto-sync list from the device" checked under the "Auto sync options" tab?

Maybe this is something I am not doing correctly, but I don't think so :-) Tracks previously synchronised via auto-sync list, are not removed from the device when subsequently unticked, and the player synched again. Also when 5 most recent .. episodes of.. is used for podcasts, older podcasts are not removed from the device when the latest podcast is added.

Ipod Touch second gen. software 2.2, win XP