Hi, I meet the same issue in debian squeeze(6.0.4) ntp 1:4.2.6.p2+dfsg-1+b1 and debian jessie (8.0) ntp 1:4.2.6.p5+dfsg-3. If /etc/ntp.conf 'server' configure is invalid server appear, if you execute /etc/init.d/ntp start will appear two ntpd process(one process user is ntp, other process user is root). Server configure is invalid I mean: server is unreachable. When stop the ntp service will stop ntpd which user is ntp. The ntpd that user is root, will not be killed.
-- Best Regards, Bo Qin