If I understand your set up, I had the exact same issue with booting from a SD Card from 5V on the VDD line ( power input ). It worked great on USB and failed with 5V power source.
So for me, I swapped the SD Card from my BB and the BBB, both known good cards, the issue went away.
All I can assume is that the SD Card that I used for the BBB was not liking that “flavor” of power. The BB had no issues with the same card!
I now have the Beagle Board Black ( BBB ) working with the 32G card that was in the Beagle Board ( BB ) and all is well. SD Cards are like that…
One more NOTE: The “Bad” SD in the BBB failed over long time periods, not right at the first boot many times. Now the system works for days.
e.m.g.