Hi Terry,

> but it looks like something is interfering with the clock when the
> server is running.

More than one thing, I expect.  It's possible your system is trying to
adjust the RTC based on the divergence it notices between boot-up and
shutdown.  /etc/adjtime can be a sign of that, or
/etc/init.d/hwclock.sh.  Then ntpd might be triggering something similar
in the kernel by reporting NTP-time is sync'd;  that's the "11 minutes"
that you've been seeing.
https://unix.stackexchange.com/questions/285129/switch-off-11-minute-kernel-mode

I don't know if dmesg(1) shows this read/write to the RTC.

Am I right in thinking that you want the Pi to treat the RTC as
perfection, never wrong, and never adjust it unless you manually set the
RTC's time?  That the RTC time should be used at boot, and thereafter
the Pi's own clock maintains the time and the RTC is read or written
again.  Any divergence doesn't matter because the Pi will reboot
tomorrow and the RTC read afresh.

You might find an rdate(1) from the slave is simpler at boot time.  I
don't know if Raspbian provides a server for the `time' port, but it's a
trivial thing.

Cheers, Ralph.

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