There is a small mistake in the new package that makes this bug not fully closed. You have missed to add -u $UGID for restart in the init script. Other than that 4.2.0a+stable-6 works fine for me, good work!
/Pär
--- ntp-server 2005-03-15 23:40:18.000000000 +0000 +++ ntp-server 2005-03-17 01:29:45.000000000 +0000 @@ -28,7 +28,7 @@ echo -n "Restarting NTP server: ntpd... " start-stop-daemon --stop --quiet --pidfile /var/run/ntpd.pid sleep 2 - start-stop-daemon --start --quiet --exec /usr/sbin/ntpd -- -p /var/run/ntpd.pid + start-stop-daemon --start --quiet --exec /usr/sbin/ntpd -- -p /var/run/ntpd.pid -u $UGID echo "done." ;; reload)