Does your USB controller show up as a controller icon when it is connected? Top/left. Some USB controllers just don't play nice with the OUYA. Are you able to play 2 player games with it? Try downloading/installing keytest.apk and seeing what kind of inputs its the ouya is receiving from it.
Every controller is different depending on what type of encoder it uses. This changes what type of device your OUYA sees it as. Also what of default keys it sends to the OUYA.
Did you make a custom kl to configure your usb controller? If no how did you go about this?
Hope this helps. If not maybe with a little more info I can help you get it figured out.