In the beagleboard or beaglebone are different modes to work the pin. With the previous kernel they are located in /sys/kernel/debug/omap_mux. Do u know with the last Kernel
Check out this set of device tree files: https://github.com/nomel/beaglebone/tree/master/gpio-header
It allows you to change the gpio mux mode on the fly.
I just tried them and they seem to work.