I think if you don't just happily accept the fact that it works now, but instead try to "get to the bottom of it" you'll probably stir the wrath of the programming gods/devils and your axo board will just go up in flames. Just leave it as is.
That being said, i definately fried a STM32F4 board from a different platform with these shitty little dupont jumper cables. Shorts on shorts on shorts. Imagine all these little electrons travelling down the wire, and then one of them sees it and is like is "fuck guys we are doomed theres a dupont ahead. Pray to the gods so at least half of us will make it through. Ahhhhhrrrrrr its not connected at aaaaaaaalllllllllll" and falling off the voltage cliff. or something like that.