I didn't mean "holding B", just pressing it. But that's when you get a "B = Stop Boot" message in the corner, otherwise you'd simply get to choose between SD / USB to show your game list; after that you can press B to toggle the settings display. It's all there in the screen.
If for some reason what you mean is that you load nintendont and it chooses the Source and the game on its own, displaying the game list, then that's something weird. When autoboot is enabled you don't see any of that, but only the button legend on the corner and after a little while the game is loaded.
If this situation keeps happening unless you spam the A button as you described before, then you should try deleting the nincfg.bin just in case.