Inconsistent GPIO values on Beaglebone Black running Debian
It's possible that one or both GPIOs are not floating. Those states that you see could be caused by the internal pullup/pulldown resisters.

Are you familiar with Debian's device tree overlays? That is what you would use to configure the I/O pins on the BBB. Besides input and output, you can configure pins for drive-strength and enable/disable pullup and pulldown resistors.

Have a look here for details:
http://derekmolloy.ie/gpios-on-the-beaglebone-black-using-device-tree-overlays/