slow calibration path on every boot on your machine.
(tscmax - tscmin) / avg = 0.064 (result from third run)
On my test machines I get values below 0.02
While it's statistically not really correct we still can use that info
to catch cases like we see on your machines.
While booting up I saw this one on the serial console..
root@quad12:~# hwclock --systohc
Cannot access the Hardware Clock via any known method.
Use the --debug option to see the details of our search for an access method.
root@quad12:~# hwclock --systohc --debug
hwclock from util-linux-ng 2.13.1
hwclock: Open of /dev/rtc failed, errno=2: No such file or directory.
No usable clock interface found.
Cannot access the Hardware Clock via any known method.
Can you provide your .config file please ?