Apple Remote App not working with Apple TV?
We had this very issue this week!
The trusty iPad could throw YouTube clips to the Apple TV but we could not use it to control the Apple TV itself using the Apple Remote App.
Answer, we had used the wired only connection to connect the Apple TV to the network (naturally we thought this would result in a faster more reliable connection), when we made the Apple TV use the wireless network the problem went away. Strange!!!