my experience is with the new apple TV and a Beo4.
I had to unpair the apple TV from the remote that it was shipped with and which I had used to install and configure the apple TV.
Once I had done that, the apple TV responded to the signals the PUC sent (that were triggered by the Beo4).
Unpairing is a configuration option inside the menu of the extreme right hand side of the apple TV's main menu screen.
First B&O (1976) was a Beogram 1500 ... latest (2011) change has been to couple the BL11 with the BL6Ks *sounds superb*