I have noticed the same problems. In fact what I notice is that when turning the BV7 off the IR emitter on the Apple TV flashes, the Apple TV turns off (the power light goes out) but the emitter flashes some more and it turns on again. Prior to having Apple remote in the PUC list I had used the learning function of the Apple TV to learn commands for another product. This worked fine although again I could not use the Genius function. It appeared to me that the issue is for the Genius function to work the button needs to remain pressed and send a constant signal. It did not appear to me while teaching the Apple TV the Beo 4 commands that the Beo 4 is capable of sending a constant signal. Pressing a button on the Beo 4 results in only one brief signal, regardless of how long the button is held down.
Beovision 7-55 with Beolab 7-4, 9s and 4000s
Beovision 10-40 with Beolab 1s and 6000s
Beosound 1, 5, 2000, and 3000
Beotime, Beotalk, Beocoms