I know it's a long time, but I'm cleaning up old NTP bugs atm.

This has multiple "fixes" and things to bementioned.
First of all it is interesting that iburst "fixes" this as it is documented as:
When the server is unreachable, send a burst of eight packets instead of the 
usual one.  The packet spacing is  normally  2  s;  however,  the  spacing 
between  the  first  and  second packets can be changed with the calldelay 
command to allow additional time for a modem or ISDN call to complete.  This 
option is valid with only the server command and is a recommended option with 
this command.

While I don't see how this helps with the "problem" it is recommended so it 
should be fine to add.
We already did add it in the past by one of the merges with Debian, so recent 
releases already have the iburst as default.

Then to close one more extra info - ntp is meant to slowly drift times, as many 
logics hat to be time warped.
That said the issue of one (and only one) huge initial time warp is a known 
thing.
The solution to that is -g to ntpd which we use by default.
Documented as:
       -g     Normally, ntpd exits with a message to the system log if the 
offset exceeds the panic threshold, which is 1000 s by default.  This  option  
allows  the time  to  be  set to any value without restriction; however, this 
can happen only once.  If the threshold is exceeded after that, ntpd will exit 
with a message to the system log.  This option can be used with the -q and -x 
options.

That means if your offset is what ntp considers huge (>1000 sec) it
warps time once, and if it is small it drifts towards it.


Also by default time is managed by systemd now, but still all old reported 
issues were fixed, juts people forgot to update - setting fix released.


** Changed in: ntp (Ubuntu)
       Status: Triaged => Fix Released

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Touch seeded packages, which is subscribed to ntp in Ubuntu.
https://bugs.launchpad.net/bugs/538840

Title:
  ntpd default config misses "iburst" / takes minutes to synchronize
  initially

Status in ntp package in Ubuntu:
  Fix Released

Bug description:
  Binary package hint: ntp

  My hardware clock is currently off during boot always (probably
  because of empty CMOS battery) and ntp takes some minutes before it
  synchronizes the clock.

  ntp should synchronize/fix the clock right after it has been started
  (as fast as possible).

  E.g. boot time is 03:39:01, ntpd start at 03:39:22 and time gets fixed
  after 03:42:53 - that's more than 3 minutes after ntpd has started.

  Ubuntu Lucid, ntp 1:4.2.4p8+dfsg-1ubuntu1

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