ITunes copies files without the "copy files to Media folder" checked.

I've never been a fan of iTunes. My dislike of its impositive ways is directly proportional to its version (10.1.1(4) currently), so I never allow it to do anything automatically for me. I really like it that way.
In recent years, after a couple of experiences filled with much tribulation, I have never checked either "Keep iTunes folder media organised" nor "Copy files to iTunes media folder when adding to library" under its Preferences, whenever I have been forced to use this accursed application.
But owning an iPod (a couple actually) makes it impossible to live a jovial iTunes-free lifestyle. So yes, I use it on occasion.
Those occasions almost exclusively mean copying music and audio books to and from it. No videos, no Pictures, no nothing else.
I'm using a 4th Generation iPod Touch.
My iTunes library is not on my computer but on an external HD.
Anything I drag and drop to the library comes from folders in that external HD.
Now, the few audio books I own are not even inside my iTunes media folder. They are elsewhere in a folder of their own. But everything had worked O.K.ish so far.
Today, while re-tagging some audio books I asked iTunes to show the file in Finder. And it did. It was indeed inside that external HD... BUT... on the iTunes media folder, not on the folder where I keep those audio books originally.
I checked the iTunes "Preferences" to see if the Gremlins had changed anything. It was as it has always been (with all pertinent options unchecked).
I checked the original folder to see if they had been moved. Nope, they were still there too.
The versions are not the same, since all that re-tagging I'd been doing had of course affected the ones in the "wrong" folder (the one I did not assigned nor agreed to create).
The music is fine (some of which comes from a folder similarly outside the iTunes media folder, although most comes from within), it's just the audio books.
An event of note is that a few days ago, that external HD had a problem and the data had to be moved elsewhere, the HD re-formatted, and the info placed back into it once more. But the paths remain identical since the HD has the same name and the folders are where they once were. I've no idea if this has any effect on anything at all, but I thought to mention it.
So this mystery is such. Any takers?
The questions are: Why does this happen? How can I stop it from happening again (aside from not using iTunes :-D).
It is not that big a problem since I have very few audio books thus the duplicate is not too large, but I'd like to know how to avoid it, if possible.
Thanks in advance for any information on this.

iTunes prefs -> Advanced. Uncheck *Copy files to iTunes music folder when adding to library*.
Any reason you don't want them in the music folder? You could add them to iTunes and delete the from your documents folder.

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