Working with the Beaglebone can be really frustrating. There are a lot of buggy libraries and incomplete docs, and the Sitara chip is really complicated, overloading its pins to do lots of different things.
Today I needed 8 GPIO pins for a test harness. I looked at the diagrams for the P8 and P9 headers and picked some likely-looking pins. I used the Adafruit_BBIO python library and set them up as outputs, then toggled them and watched with the meter. Three of them didn't work.
So I changed my script to try to toggle *all* the pins on P9, even the ground and VCC pins. Of course this doesn't bother Adafruit_BBIO because it has no error checking (ugh). Here are the pins that worked as GPIO outputs.
Note that this is from my Beaglebone *Green*. On the Beaglebone *Black* you'd probably need to disable HDMI for some of these pins to work.
Beware: I repeated this test several times across reboot and power down, and some of the pins worked the second or third time that didn't work the first. It's possible that's sloppiness on my part, but my intuition says no, and that Adafruit_BBIO isn't initializing the pins correctly, so there's some random chance at play. The best reference I've found so far in how stuff actually works is "Exploring Beaglebone", which is unfortunately a non-free book, but very well written.