Changing the media folder location doesn't move anything. If you want iTunes to consolidate to the new location it will make new copies but leave the old ones behind. If you already moved copies there that aren't connected to iTunes then when it consolidates it make new copies rather than overwrite the unexpected files. Splitting your media folder from the library files isn't generally the best way to do things. Usually I would recommend moving the entire iTunes folder to the new path and accessing it by holding down shift as your start iTunes, but since you've already started it may be too late for the simple approach.
Where is your library now? Where did you want to move it to? Does your library contain duplicates?