I recently switched from using an Airport Express to an Apple TV for streaming audio into my main system. I am using Apple Lossless files and feeding that into a Bryston BDA-1 DAC via the optical link. I did notice that when I switched the Byrston changed from showing locked on 44k1 to 48k0. When I play music onkyo dvd player through the BDA1 it also shows 44k1. Don't know if that can make the difference you are hearing but Apple TV apparently outputs at a higher sample rate that an Airport Express.
Apple TV sound quality as a transport
I recently switched from a DVD Changer into a Channel Island DAC to an Apple TV into the same DAC. I was under the impression that the DAC was ultimately responsible for the sound but I swear it actually sounds better. The only change other than the Apple TV is the switch from coaxial from the DVD to optical from the ATV. Is it possible that the ATV sounds better than my DVD changer as a transport?