Check out the following:

Bone VDD_3V3EXP Disable Issues

BBB battery connected doesn't powerdown VDD_3V3EXP P9_3/4.

BBB operation with battery

There's a bunch more references, but this describes a hardware fix.

On Monday, April 13, 2015 at 12:14:50 PM UTC-7, jean....@dazedstudio.com 
wrote:
>
> Hi everyone,
>
> we are running for our project a BBB on Debian (stock image and updated 
> kernel to bone71) on a battery setup. In our circuit, we have an external 
> RTC that wakes up the BBB on a set interval to do reading and then close 
> back down. Our problem is that sometimes the CPU shuts down but not the 
> PMIC (TPS65217). At that moment, any signal on the power button is ignored 
> but the reset button still works. On the BBB, the power LED is lit up, but 
> all user LEDs are closed down.
>
> Has any one had simliar problems or is there any known fix for PMIC 
> problems? 
>
> Thank you for your help.
>

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