OUYA is working on it. Also have that problem.
Answer from OUYA (they answered 7 hous later on a saturday!)

Chris Green (OUYA Support)
Jul 13 10:39 (PDT)
Hi Geko,
We are currently working on fixes for this issue however for the meantime, somethings you can try would be:
1. make sure the OUYA is not enclosed in an entertainment center or otherwise
2. try to keep the distance between console and controller to a minimum
Please let us know if you still have any difficulties.
Hope this helps!
- Chris
OUYA