Still have the same issue as multiple users reported, though I'm running a quite recent BBB image U-boot. I also do not experience it every time, it seems to be some timing issue or something?
Aug 9 06:51:38 : [ ... ]
Aug 9 06:51:38 : GPIO.setup(io, GPIO.IN)
Aug 9 06:51:38 : ValueError: Set gpio mode failed, missing file or invalid permissions.