It seems that from time to time amanda will loose connection to some servers running Ubuntu.
In the daily amanda mail report, there will be lines like:
puffer1000 / lev 0 FAILED [Request to puffer1000 failed: timeout waiting for ACK]
and an amcheck -c on that host will return an error.
This can be cleared by restarting inetd on the affected servers:
sudo service inetd restartor xinetd on firewall:
sudo service xinetd restart
There is a very twisted automation on Ubuntu that overwrite the contents of /etc/ined.conf (linked to update-inetd; they really have to mess up with everything) so I changed to using only xinetd.