Apple TV or Direct USB Connection to cpu

I just purchased the new 1080P Apple TV. I have it hooked up via a Wireworld supernova 6 toslink to my MHDT Constantine Plus dac and it sounds great playing my itunes library on my computer. Just for fun I bought a $2 generic usb cable and hooked it up. This is crazy but I think the usb actually sounds better with a direct connection to my cpu. Anyone else have thoughts on what sounds better?
The ATV 2 output everything in 48 kHz rather than the native 44.1 kHz. Not sure about the newest ATV, but it's most likely doing everything at 48 kHz too. Perhaps this explains some of the difference, as from USB may be the native 44.1. I don't know how much audible difference that change makes, but it can't be argued that the original file isn't being altered.

Also, maybe the computer through USB has less jitter than the ATV.

I have an ATV 1. Haven't tried USB to compare, as my laptop is nearing 9 years old and has some issues when playing music nowadays.