You can edit your defaults file to run ntpd at maximum priority:

--- /etc/default/ntp~   2009-12-04 13:07:15.000000000 -0500
+++ /etc/default/ntp    2010-02-09 17:56:07.000000000 -0500
@@ -1 +1 @@
-NTPD_OPTS='-g'
+NTPD_OPTS='-g -N'

-- 
ntpd should run niced
https://bugs.launchpad.net/bugs/229632
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