I just tried 5 Cm Per Second's soundtrack (it's an Anime OVA). The soundtrack is almost all quiet piano. Aaaand no crackle. Must have just been the other recordings. Both crackles happened on a Miyazaki soundtrack and the Girl who Leapt Through Time soundtrack. Must have just been distorted recordings. What a shame, I love those ones. I'll still listen to them, but those crackles are a tad bit annoying.
My god, I'm constantly being blown away by how much detail these cans pick up.
EDIT: You know, going back and listening...I realize that both times the crackle happen on those other ones, it's during a hard piano note and a violin string vibrating harshly at the same time. It's almost as if, both frequencies are so loud and happening at the same time, they make the crackle effect. I'm not sure if that makes sense. Either way, I'm certain it's the recording now. Because other soundtracks with strings and piano isn't making the sound. Just those ones.
If you lower the volume, do you still hear the crackle? Do you have different gain controls in your audio chain?