Hi there, sorry for the delay, didn't have a Beast at hand.
I tested it now, and running the program at boot when powering from the 5V barrel jack works just fine for me. Also, having Digital 0 (P8.07) or Digital 1 (P8.08) connected to 3v3 does not prevent the board from booting for me (which is the expected behaviour).
I am using Bela Image v0.3.8a, but I don't expect the result to be different with any of the others.
Is it possible that the issue could be specific to the program you are running? If the problem persists, would you be able to share it with me?