I have a BBB that will not reliably boot after shutdown -h now is issued. In order to minimize power consumption between periodic events the unit is shutdown and then restarted by an external clock that momentarily pulls down the power button. Approximately 1/20 times the unit will turn the power LED on boot never start the boot process where the LEDS are flashing. The unit will not respond to either Power or reset buttons in this mode.
In this case, the power supply is always on
Thank you for you assistance,