I have the same problem. Using Lubuntu 14.04- 0.9.1 img for Orange pi lite.
bin2fex in sunxi tools gave me "malformed data" error.
using the windows bin2fex gave me "unrecognized GPIO port #12".
Since this bin2fex is so critical in setting display, audio, resolution, etc. This bug made my ARM experience very bad.
I understand and appreciate all the efforts in the linux community though.