Sorry, nothing suspicous in the logs (syslog, boot, debug, dmesg, kern.log,
messages).

$ lsmod | grep -i rtc
genrtc                  8180  1

genrtc? Indeed, /var/log/dmesg reads "Generic RTC Driver v1.07".

$ modprobe rtc
FATAL: Error inserting rtc 
(/lib/modules/2.6.10-bs2/kernel/drivers/char/rtc.ko): No such device

Huh? I stopped chronyd, removed genrtc, inserted rtc and restarted chronyd
(with rtcfile enabled). Youhou! No more freezes with
$ lsmod | grep -i rtc
rtc                    10424  1 

Okay, so how to make sure rtc is inserted instead of genrtc? Not really
chrony's role, but its default config file is not "safe". A debconf
information or question could be useful here.

-- 
Daniel Déchelotte
                  http://yo.dan.free.fr/

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