Took a day longer than i had hoped but i finally got the Ouya version of Crime in Progress to work with controller support on Ouya.
After racking my brain i found this...
Ouya SDK: Unity input joysticks do not work when the Ouya SDK is installed
When the Ouya Everywhere SDK is installed in the project, it interferes with Unity's input system on Android builds preventing any joystick axes or buttons from working. At present, there is no known solution to make Unity input work on Android when the Ouya SDK is installed.
Sure enough i was using the Ouya SDK, once removed, controller support that worked in the Unity editor worked on the Ouya.
Just a heads up to anyone that may have faced the same issue.