System Clock is updated before the TAI-UTC offset is applied for PHC source in chrony 6.4.1

Hi,

Before I send a lot of detail I wondered if anyone had seen this
phenomenon. I have just upgraded my local chrony server to Trixie on
RPI 5 with chrony 4.6.1.

I had previously been using the ethernet NIC clock as a time source
with ptp4l and phc2sys, which worked fine.

During the upgrade I changed to leapseclist from leapsectz as the
latter does not work on Trixie.

The issue is that on startup the system clock is set by the PHC source
before the TAI-UTC adjustment has been applied which means it jumps
36+ seconds one way and then back again during the startup. This
obviously trashes the PHC as a source, and it didn't happen
previously.

Essentially PHC is chosen as the source, updates system clock (wrong
by ~37s) then the TAI-UTC adjustment is found which causes system time
to jump again in the opposite direction by ~37s

I can see this using systemctl status chrony or using journalctl.

I have currently turned PHC off again - but happy to turn back on and
send any logs etc that might be useful.

The other source is PPS from GPS, which is even more accurate on the
new versions :-)

Thanks
Simon

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