Funny you should mention that. I have the same thing with some audiobooks. But not on my music. I thought it was something with my files, but I get it on other files that are not related to.
I thought it might have been that the audiobook files have a newer ID3 tag version than the music files and that the exstra id3 info gets played as sound? It looks like my audiobook files have ID3 version 24 and my music have 22. These are mp3 files. Another thing is that the crack sound variates in strength and length. From quite loud to nearly nothing. But the length is always quite smal but with only small differences.
Now, this with the ID3 thing is purely guessing. It just poped into my mind.