1) Install the application, do not forget to run the Controller Monitor application at least once to set the timeout and ensure the service is installed. Again, you do not NEED to do anything in the app other than launch it and then press (A) to leave it.
2) To ensure the service is running completely power down the OUYA and power it back on, with out any controllers plugged in and none of the wireless controllers powered on. Wait the prescribed time, again you can change this in the application, but by default it is 3 minutes. Do note that this is 3 minutes from the time the OUYA is completely booted. it should then take you to the pairing screen. If you are not taken to the pairing screen from here please let me know as something is wrong.
3a) For wireless devices, completely power down the device and then turn it back on. Turn on the controller and see if the pairing screen still comes on. If it does please jot the controller make down so we can track it.
3b) For wired devices, completely power down the OUYA, plug in the controller and turn the OUYA. See if the pairing screen comes on. If it does please jot the controller make down so we can track it.
The reason I need this is each controller has a specific controller ID, currently I am just searching for the word "controller", but this may not be enough for all of them.