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Date: Sat, 20 Jun 2015 15:50:49 +0300
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> Тогда, вообще, непонятно.
>
> Имеем ядро 3.14.27-std-def-alt1
>
> # hwclock --localtime --systohc
> # hwclock -r
> Fri Jun 19 09:54:53 2015  -0.860046 seconds
> # date
> Fri Jun 19 09:54:57 SAMT 2015
>
> Далее делаем так
> # service ntpd start
> Starting ntpd service:                 [ DONE ]
>
> и ждём:
> # sleep 900 ; hwclock -r
> Fri Jun 19 06:13:40 2015  -0.813063 seconds
>
> Ядро плевать хотело на /etc/adjtime
>
user@eee2 ~ 14:52:56> sudo sh -c 'hwclock --localtime --systohc; hwclock 
-r; date; service ntpd start; sleep 900; hwclock -r'
Sat Jun 20 14:56:04 2015  -0.719747 seconds
Sat Jun 20 14:56:04 MSK 2015
Sat Jun 20 15:11:05 2015  -0.563081 seconds

Может вам надо обновить ядро?