Sorry, coming late to the party. I just downloaded the mp3 version of Eric Whitacre's "Water Night" album from Amazon and experienced the faint flutter or tremolo you describe. I tried playing the files in Windows Media Player, the Amazon Cloud Player, and iTunes, all with the same result. I then bought the same album from iTunes and it does NOT have this problem, whether played in iTunes or Media Player.
Curiously, though, I tried listening to some demo samples of Whitacre's "Light & Gold" album on iTunes and got the same flutter business (noticeable on "A Boy and a Girl") - then went to the same song on a different Whitacre album ("Cloudburst") on iTunes - no flutter.
Anybody else witnessed this?