After booting Debian for Beaglebone Black I looked at P9 pin 12 (GPIO 1 28) on an oscilloscope, their is a positive 65ms wide positive pulse that repeats approximately every second.
Is this pin not set up as a GPIO pin?
I tried
echo 60 > /sys/class/gpio/export
However when I tried
ls -al /sys/class/gpio
after this gpio60 did not show up.