There if definitely some controller weirdness going on for some setups that isn’t straightened out. I’ve tested this using and OUYA console with an OUYA controller, wired XBOX 360 controller and Dualshock 3 and I haven’t had issues with those. My OUYA hardware is all kickstarter edition stuff, so I’m not sure if there is an issue there (I would think not, but…).
I didn’t use any OUYA dev kit code on this game, everything is written all bare metal android Java, and I know from testing that if I install on a non-OUYA device (like my android phone) and use an OUYA controller with that, it DOES NOT work, but I have another non-OUYA controller that I use with my phone and if I use that it acts as expected. I believe this has to do with a custom key layout file that OUYA’s have for use with their controllers, but other android devices don’t have these (and I believe you have to have root access to your device to add it).
The project wasn’t originally intended for OUYA and I didn’t feel like I had time to incorporate it, I hypothesize that if I incorporate their controller APIs that these problems will go away. Hopefully I’ll have time to take that on in the near future.
I’m curious if what you are seeing falls into anything I described in this post or if it’s something else.