The board is connected to a 5V power supply, to a USB hub and via Ethernet 
to a router. It has no capes.

uname -a
Linux beaglebone 4.4.39-ti-r75 #1 SMP Thu Dec 15 22:16:11 UTC 2016 armv7l 
GNU/Linux

The command

  sudo systemctl poweroff

reboots it just like 

  shutdown -P now

However, if the board is disconnected from the USB hub (still connected to 
the power supply), both of the above commands shut the unit down as 
expected. I checked this several times: connecting even a running unit to 
USB makes it unable to shutdown. However, if powered from USB (power supply 
disconnected) the board shuts down again without a problem.

I tested this several times and it seems, that the only combination where 
the board can not shut down is when connected to both the power supply and 
USB at once. Which is ok as of me, as I do not need the USB connection any 
more.

There is an old thread (the kernel must obviously have been different) 
where a similar problem is reported by several people: 
https://groups.google.com/forum/#!msg/beagleboard/qw5zlS4F4p4/chu0J3VXKgAJ


On Wednesday, April 26, 2017 at 4:45:41 AM UTC+2, Graham wrote:
>
> What OS/kernel is ithinu running?
>
> "shutdown -P now" works on all my BBB/BBG boards.
>
> But, I run from external +5V, without anything on the battery connections.
>
> --- Graham
>
> ==
>
>
>> I usually tell everyone to use:
>>
>> sudo systemctl poweroff
>>
>> as systemd knows how to tell the external tps65217 to cut power.
>>
>> looking at the syslog, i don't remember any issues with 4.4.39-ti-r75,
>> and looking at the git log i don't see any poweroff regressions
>> mentioned..
>>
>> Regards,
>>
>> --
>> Robert Nelson
>> https://rcn-ee.com/
>>
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>
>

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