I have a triple boot with OS X El Capitan, Windows 10 and Ubuntu. As I expected there are problems with the clock, but unexpectedly the culprit seems to be Ubuntu.
I've been running a series of restarts, booting a different OS each time and checking the time in the BIOS in between and these are my results:
Restarting from Windows, the BIOS time is in UTC as expected (since I already did the registry hack).
Booting Ubuntu. At the login screen the time is incorrect, it shows the UTC time. After log in the time seems to be synced (probably by NTP).
Running hwclock and timedatectl tells me the hardware clock is in UTC.
Restarting. The BIOS time is local. Why!?
Booting OS X. Magically the time is correct (probably thanks to a NTP sync).
Restarting again. BIOS time is UTC.
Booting Ubuntu and same thing happens...
What's is going on? Maybe the NTP server is giving time in local timezone?
Update:
Ok, after the last state I booted again into Ubuntu. Now timedatectl still shows the time is in UTC, but hwclock reports the local time a really weird time, two hours more.
Local time: dom 2016-09-11 13:25:21 CEST
Universal time: dom 2016-09-11 11:25:21 UTC
Timezone: Europe/Madrid (CEST, +0200)
NTP enabled: yes
NTP synchronized: no
RTC in local TZ: no
DST active: yes
Last DST change: DST began at
dom 2016-03-27 01:59:59 CET
dom 2016-03-27 03:00:00 CEST
Next DST change: DST ends (the clock jumps one hour backwards) at
dom 2016-10-30 02:59:59 CEST
dom 2016-10-30 02:00:00 CET
This is the output from hwclock
hwclock de util-linux 2.20.1
Utilizando /dev interface to clock.
Se presupone que el reloj de hardware tiene la hora UTC.
Esperando señal de reloj...
...recibida señal de reloj
Hora leída del reloj de hardware: 2016/09/11 13:34:51
Hora del reloj de hardware: 2016/09/11 13:34:51 = 1473600891 segundos desde 1969
dom 11 sep 2016 15:34:51 CEST -0.469825 segundos
The last output should be the time displayed in the clock, but no, the time displays the hardware clock, which right now is in local time.
Update:
Ok I think I already know what happens. The clock that displays on the top-right shows the hardware clock for some reason. After the login, it syncs and changes the hardware clock, but hwclock still reports the previous time. That's why when booting again into Ubuntu the report of hwclock changes but not the time displayed.
I will give also some background information I have Ubuntu 14.04 and I've been warned about the HWE EOL, that's why I updated to the latest kernel (4.4.0-36). I think the issue was produced by that update
timedatectl(please [edit] your question to add it) and in which time zone are you geographically located? – Byte Commander Sep 11 '16 at 11:09