Some authoritive information:
Improper Power Down….All Revisions
We have been noticing a very small number of boards that are experiencing power issues, where the LED flashes and the board does not power up. We have been chasing this for a while now and due to the small number of boards that have the issue and the fact that the issue can also be caused by having things connected to IO pins not powered correctly, it has been hard to nail down. Our initial take was that it was a manufacturing issue on some boards, but we could never prove that. Based on the latest information we have gathered, this appears to be an instance where the PMIC does not power down the processor in the right order due to the violent removal of the power cables, either USB or DC. So, we are recommending that the power button be used to power off the board or by issuing the Halt command. After that you can remove the power cable. If everyone follows this process, we should see a decrease in these issues, but it will take a while for the results, either good or bad, to show up. This will also help prevent the contamination of the eMMC and the SD cards by allowing the kernel to shutdown properly before power is removed.
It’s going to be hard to follow these instructions with my system living in a Hunter outside enclosure.
I’m going to look more closely at the battery support on the BBB board.