If ntpd is running, ntpdate should never run - doing so causes clock jumps. In Trusty, /etc/network/if-up.d/ntpdate actually stops ntpd so ntpdate can run. Debian jessie doesn't do this, so if this was from upstream, it's been fixed.
From /etc/network/if-up.d/ntpdate:
-----
if [ -e /usr/sbin/openntpd ]; then
service='openntpd'
else
service='ntp'
fi
If ntpd is running, ntpdate should never run - doing so causes clock jumps. In Trusty, /etc/network/ if-up.d/ ntpdate actually stops ntpd so ntpdate can run. Debian jessie doesn't do this, so if this was from upstream, it's been fixed.
From /etc/network/ if-up.d/ ntpdate: 'openntpd'
-----
if [ -e /usr/sbin/openntpd ]; then
service=
else
service='ntp'
fi
invoke-rc.d --quiet $service stop >/dev/null 2>&1 || true
/usr/sbin/ ntpdate- debian -s $OPTS 2>/dev/null || :
invoke-rc.d --quiet $service start >/dev/null 2>&1 || true
------
Workaround: if-up.d. disabled if-up.d. disabled/ ntpdate --rename /etc/network/ if-up.d/ ntpdate
sudo mkdir /etc/network/
sudo dpkg-divert --divert /etc/network/