After adding folders to iTunes library, now have duplicates of each song

I store all my music on a separate drive, M:\
I have a specific file structure setup that has worked for me for years, M:\Artist\Album
I recently received an iPod for my birthday, and started using iTunes. After adding my music drive (M:\) for inclusion into the library (without "keep..." and "copy..." selected, as to keep my current file structure intact), when selecting "File->Display Duplicates" just about every song in the library has a duplicate, one in the original folder "M:\Artist\Album", and another in "M:\Playlists\..\Artist\Album". I understand that basically somehow iTunes glitched and started in the "M:\Playlist" directory when adding to the library at some point, however I am at a loss as to how. In my actual folders I only have 1 copy of each song, so basically iTunes is making a symbolic link to each song and adding it into the library as a separate song.
I have over 9000 (must...resist...meme...) songs in my library, and removing and restoring takes quite a while. I'm pretty sure I'm going to have to do this at least once now, but any ideas as to why or advice on how to avoid this particular problem in the future?
I am pretty set in my ways of my current file structure, since I don't use iTunes as my primary media software, so I would prefer to not have to resort to succumbing to just letting iTunes handle everything the way it wants (I pretty much hate that).
Thank you for any suggestions you may have.
EDIT: Is there a way to have iTunes rename/move files when adding to its library to specific folders via custom rules based on ID3 information (i.e. WMP rip settings)?
Message was edited by: kaziekama

If you have "Keep..." and "Copy..." unchecked, iTunes will simply reference the existing file, and will not change your file structure, as you correctly note.
I'm fairly sure that some other program is operating on your files. The "Playlists" folder that you mention has nothing to do with iTunes. On my PC, only Windows Media and Roxio use it.
To your question +"Is there a way to have iTunes rename/move files when adding to its library to specific folders via custom rules based on ID3 information (i.e. WMP rip settings)?"+ the answer is no. When iTunes rips a CD, it names the files as track number and title, with no option to do differently. And as far as placing the ripped files, they go in Artist/Album, with no option to do differently. As full-featured ripping programs go, iTunes is not even in the race.

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After adding folders to iTunes library, now have duplicates of each song

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