Artist folders removed from iTunes music folder

[jcloughesy]

My computer will randomly remove remove an artist folder from my iTunes music folder and place it in my Macintosh HD folder, next to Applications, Library, System, and Users. It seems like it almost creates a whole new Home folder because in order to get to the music I must go through a folder titled JC (the name of my home folder), then Music, iTunes, iTunes Music, Music, and then the artists (I realize this sounds confusing, I'll attach a picture to better explain). It seems as if the artists that are removed from my iTunes music folder are artists that I remember recently playing one of their songs.
Anyone know why this happens and how to stop it?

 

[cloroxbleach4]

Where do you have your itunes set to put your music? Does it itunes make a separate copy when you add new music?

 

[jcloughesy]

iTunes saves music in /Users/JC/Music/iTunes/iTunes Music. It seems to make a duplicate folder starting with JC-->iTunes Music (seen in the picture) of a few random songs.
I have the option copy files to iTunes Media folder when adding to library checked but I don't think it makes any additional copies