I went through a period of finding the highs from my VDA-2 based system quite "rough", but then I plugged the switching power supply of my squeezebox SB3 into a different circuit, and they got a lot cleaner, smoother and better resolved. Makes me wonder about your AppleTV ...
My speakers are Thiel CS .5s, whose tweeters are notoriously unforgiving.
I never did completely figure out which components in my system were affected by what I assume was RF noise pollution, but it wasn't completely confined to the VDA-2, because I thought I heard some improvement in vinyl sound as well. I'm pretty sure my Van Alstine power amp (an Omega III) was quite sensitive to the problem.
I know some people believe you can get RF pollution along the digital signal path as well (perhaps an argument for one of Dusty's SB3 power supplies), but if I have that problem it's awfully subtle.
Hope this helps ... the realization certainly helped me. Oh, and not that long ago I would have been very skeptical if someone had told me that this was the problem.