We're now running the latest Moodle 1.6.2+ to resolve previous issues with automated backups, but there are still a few problems with some contrib modules (which we have also now upgraded to the latest versions on the advice of Petr Skoda (http://moodle.org/mod/forum/discuss.php?d=48756)):
Restoring from a scheduled backup results in no links (only icons) for Books, Dialogues and Objects. There are links in the Activities block to these activity types but clicking on them gives the error e.g. 'There are no dialogues'.
Restoring from a manual backup gives functioning links for Books, but nothing at all (not even icons) for Dialogues and Objects.