Hi R,
I'm waiting to have my BS3 software upgraded to be able to control my Apple TV which is working fine with the Apple Remote. Reading your query string, I just want to refresh a couple of thoughts:
1. You have an IR cable connected from the BV7's control output to the 'eye' of the Apple TV's IR pickup. This cable either covers the Apple TV's 'eye', or almost does so (to allow it to work with an Apple remote too).
2. You have added the 'Apple TV' selection in your STB list to one of the choices in your system, such as 'PC' or 'VMEM' and selected the choice to use the Apple TV.
3. You have checked the Apple TV works fine with its own remote when plugged into the BV7. You haven't mentioned this in the string. I use 720p for the resolution.
Good luck!!