I find that xntp does not adjust the realtime hardware BIOS clock, only the system clock. Over time, if a significant skew builds up, on the next reboot the clock will be thrown back. If the master is rebooted, when there's a skew, all the slaves will get their clocks reset. If the slave is rebooted, several minutes will go by, then the slave's clock will be jump by a large amount, when it is resynchronized with a master. Solution: add the following to /etc/rc.d/init.d/xntpd, after the killproc that stops the daemon: /sbin/hwclock --systohc This will adjust the hardware clock with the accumulated skew, before the system shutdown.
xntpd should update the RTC itself. Are you running on Compaq ProLiant hardware? I think i noticed this problem on ProLiants (hwclock --systohc being unable to update the RTC).
*** This bug has been marked as a duplicate of 1142 ***