Did you find a solution? I'm having the same problem. It seems that during 
boot the /etc/timestamp is used to set the hwclock. I suspected the 
boot_script.sh file but after changing it the problem remained. I can set 
the timestamp during a shutdown but I would rather see a more general 
solution. 

 Regards,
Wim

On Wednesday, June 11, 2014 at 4:24:02 AM UTC+2, Justin Morgan wrote:
>
> I am using a BBB running the new Debian image. I have connected a DS1307 
> RTC (via a "Tiny RTC I2C modules" breakout board) to I2C2, and have added 
> "cape_enable=capemgr.enable_partno=BB-BONE-RTC" to uEnv.txt such that my 
> BBB does see this RTC as /dev/rtc1.
>
> I want to synchronize the system clock from *this* RTC on boot (and not 
> the BBB's rtc-omap that is registered as /dev/rtc0), so I modified 
> /etc/init.d/hwclock.sh such that HCTOSYS_DEVICE=rtc1. I thought that should 
> do it... *after all, I was able to get a Raspberry Pi running Raspian to 
> synchronize with a DS1307 on boot following these instructions: *
> *http://blog.elevendroids.com/2012/12/setting-up-hardware-rtc-in-raspbian/* 
> <http://blog.elevendroids.com/2012/12/setting-up-hardware-rtc-in-raspbian/>
>
> However, my BBB keeps synchronizing with rtc-omap on boot... and doesn't 
> seem to be running hwclock.sh, either (time after boot is back in May, not 
> the current time as I confirm by sudo hwclock -r -f /dev/rtc1).
>
> So where is Debian actually synchronizing the time in the boot process, 
> and how do I tell it I want to use my battery-backed clock?
>

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