When you open up the same music file from a different location, Media Player will think that it is a new song and will add it yet again to your library resulting in various duplicate entries.  As you can see, if you move your music around a lot, such as after you organized the file structure, you can end up having duplicate entries in your Windows Media Player libary with some of the entires pointing to files that are now in a different location. To fix this problem, you are going to want to compleatly remove the library file so that it can be automatically regenrated.  To do this, follow the steps below:

If you have Windows Media Player started, close it so the library file will not be in use. 
Navigate to X:\Documents and Settings\All Users\Application Data\Microsoft\Media Index with Windows Explorer or using My Computer.
Locate the wmlibrary...db file and erase it.
Start Windows Media Player once again and hit F3 once it has started up.
Enter the location that you music is and Windows Media Player will create a new library.
Now you do not have to worry about duplicate entries and entries and point to moved files in your music library.