ntpdate doesn't parse the /etc/ntp.conf file. The program ntpdate-debian is provided that reads its server list from /etc/default/ntpdate or alternatively from /etc/ntp.conf. ntpdate is run whenever a network interface is brought up. To adjust this behavior, the file /etc/network/if-up.d/ntpdate should be edited. Note that ntpdate is *not* really intended to be used by hosts with good network connectivity. The "ntp" package, which provides a persistent daemon that does a better job of keeping system time than even a cron'ed invocation of ntpdate, is a better choice for systems with good network connectivity. If all you want is to set the clock to a reasonable value once in a while, a more light-weight package like "rdate" can also do the job.