since (at least on debian/ubuntu default installation) the homedir for user “nagios” points to /var/run/nagios the known_hosts file is lost after a reboot and check_by_ssh refuses to connect to any configured ssh-machine…
make sure to connect to all ssh-targets as user “nagios” and especially have a close look to connect exactly the same way as the nagios-process does (DNS-name / IP-address)
see also: check_by_ssh-booster