Sometimes ITunes app for Windows leaves some songs in the iTunes Media/Downloads folder instead of moving them to the appropriate location within iTunes Media/Music (for me it seems to happen randomly, about 1 of 3 times).
To resolve the glitch it’s not enough to right click the song and consolidate files. Nor you can simply use Windows Explorer to move the song from one folder to another as this might break the connection between the song file and the store (ITunes won’t remember that the song was actually purchased) and/or song information is missing from inside the file (this is useful if you use other software to play your songs).
To resolve the issue, I found a workaround tough: go to Preferences window (using Alt+E to open the Edit menu) in ITunes app, uncheck the checkbox for maintaining the iTunes Media folder organized, and click OK, then go to Preferences window again and check it back. Upon selecting OK one more time, you’ll get your files moved to their correct destination folders and internally populated with the required information.