Songs in Library are Not in iTunes Music Folder

I just had to Re-create my iTunes Library, which took quite some time since each song had to be selected individually and imported (per the instructions). Anyway, I have the box checked in Edit>Preferences>Advanced to automatically Copy Songs in Libary to the iTunes Music Folder; however, I just purchased two new songs and when I went to the ITMF to check to see if they were there neither the artists nor the songs are there. I then tried to add them manually by clicking on Add File to Library, but that did not add them to the iTunes Music Folder.
If anyone knows what I need to do and why iTunes is not automatically adding the new songs to the iTunes Music Folder, please let me know how to fix this.
Thanks.

Ardwych
Yes, itunes just sets a pointer to the Windows files in its ITL database.http://support.apple.com/kb/HT1660
If you have itunes preference to copy files to your itunes music folder, then it does copy them there and you might now have two copies of the same song. But itunes will probably be using the copy in the itunes music folder.
This section of this article might explain it better
*How iTunes Manages Media Content*
http://www.ilounge.com/index.php/articles/comments/moving-your-itunes-library-to -a-new-hard-drive

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