My friend noticed the same thing. I've tested it, here's result.
Kubuntu runs two instances of ntpd when /etc/init.d/ntp-server script is run on 
system startup.

[EMAIL PROTECTED]:~# date; ps aux | grep ntpd
Thu Jan 25 23:30:05 CET 2007
ntp       4851  0.0  0.3   3732  3732 ?        SLs  23:23   0:00 /usr/sbin/ntpd 
-p /var/run/ntpd.pid -u 110:117
root      4880  0.0  0.1   3732  1048 ?        S    23:23   0:00 /usr/sbin/ntpd 
-p /var/run/ntpd.pid -u 110:117
root      5405  0.0  0.0   2812   776 pts/2    S+   23:30   0:00 grep ntpd

Now lets stop it. Only one instance is stoped by the script.

[EMAIL PROTECTED]:~# date; /etc/init.d/ntp-server stop; ps aux | grep ntpd
Thu Jan 25 23:31:30 CET 2007
 * Stopping NTP server...                                                       
                         [ ok ]
root      4880  0.0  0.1   3732  1048 ?        S    23:23   0:00 /usr/sbin/ntpd 
-p /var/run/ntpd.pid -u 110:117
root      5431  0.0  0.0   2812   772 pts/2    S+   23:31   0:00 grep ntpd


but lets wait a while, and ...
[EMAIL PROTECTED]:~# date; ps aux | grep ntpd
Thu Jan 25 23:32:11 CET 2007
root      5438  0.0  0.0   2812   768 pts/2    S+   23:32   0:00 grep ntpd


Now lets start ntpd.
[EMAIL PROTECTED]:~# date; /etc/init.d/ntp-server start
Thu Jan 25 23:34:02 CET 2007
 * Starting NTP server...                                                       
                        [ ok ]


Everything looks ok.
[EMAIL PROTECTED]:~# date; ps aux | grep ntpd
Thu Jan 25 23:35:22 CET 2007
ntp       5456  0.0  0.3   3708  3708 ?        SLs  23:34   0:00 /usr/sbin/ntpd 
-p /var/run/ntpd.pid -u 110:117
root      5462  0.0  0.0   2808   764 pts/2    S+   23:35   0:00 grep ntpd


ii  ntp                                    4.2.0a+stable-9ubuntu2         
ii  ntp-doc                                4.2.0a+stable-9ubuntu2    
ii  ntp-server                             4.2.0a+stable-9ubuntu2              
ii  ntp-simple                             4.2.0a+stable-9ubuntu2              
ii  ntpdate                                4.2.0a+stable-9ubuntu2               

My friend has found the solution. 
(http://thread.gmane.org/gmane.linux.debian.devel.bugs.general/202577/focus=202577)

-- 
Two instances of ntpd are launched, only one is stopped by the init script
https://launchpad.net/bugs/50406

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