Not booting from shutdown

We are having a problem with a BBB that will not reliably boot from shutdown after a power button is pressed.
In order to minimize power consumption we are shutting down the unit and then using an external timer to bring the unit out of shutdown. On approximately 1 out of 20 cycles the unit powers back up turns on one led but nothing else happens and nothing is sent to the console port. The unit will remain in this mode indefinitely and will not respond to power button or reset button pushes.

Can you provide some details on the voltage rails and reset signals when in this state?