The Nagios plugin "check_ntp_peer" from Debian package "nagios-plugins-basic" is not very nice. It shouts at you about LI_ALARM bit and negative jitter all the time after a machine reboots despite everything actually being fine.

result=$(/usr/lib/nagios/plugins/check_ntp_peer [email protected])

if echo "$result" | egrep 'jitter=-1.00000|has the LI_ALARM' >/dev/null; then
	echo "Unknown state after reboot."
	exit 0

echo $result
exit $status
Using above wrapper you get rid of the warnings.