An update:

For the A6 (Beaglebone Black) version, I connected U4 pin 1 (enable) back 
to VDD_3V3AUX (same as A5C).  It now shuts down correctly while on 
battery.  This was verified on two A6 BBB.

The mystery is what causes the VDD_3V3A to hang up on the A6 version when 
shutting down while on battery.

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