Random iTunes library problem or bug with duplicates

iTunes (Mac) spontaneously creates duplicate songs and does some unusual things in the process. The duplicate songs only appear in my library, the music media remains intact most of the time. Sometimes iTunes moves one or two songs from the same recording to a separate folder and puts in outside the iTunes Media folder.
The duplicate songs that appear in the library appear randomly. Sometimes both dup songs play fine, even though there is only one source file for the song. Sometimes only one plays, so I have to delete the one with the exclamation mark. Often one of the 2 dup songs has the wrong artwork. This wouldn't be a big issue if I didn't have such a large volume of music and this wasn't happening to hundreds and hundreds of songs, which need to be dealt with manually one at a time.
I have several music folders (CD , Downloads) inside the Master iTunes Media folder on the ext HD
In iTunes Perfs I have enabled "Keep iTunes Media folder organized" and "Copy files to iTunes Media folder." This setup worked fine in the past, before 2010.
I've repaired permissions regularly and have repaired the Boot HD.
I first starting noticing this problem at some point in 2010 while using iTunes 9. Upgrading to iTunes 10 has not helped.
Any ideas on what's going on or what I might try to fix the problem?
Is this a bug in iTunes?
If I re-installed iTunes and could return to an earlier version which one should I use ?
Specs. iTunes 10.3.1 with 350 GB of music on an external HD

Thanks for taking the time to respond to my question.
I need some clarification on your instructions. Once I have Exported my Library to the desktop and moved my iTunes folder to the desktop I can't proceed as you suggest.
When I open iTunes it opens the original library full of all my music. If I launch iTunes (while holding down C key) I can create a new empty iTunes Library inside the Music folder.
If I try to import (open) the original Library.xml file on the desktop nothing happens. If your saying I need to import all the music in my iTunes folder (inside the Music folder) I can't do that since all my music is on an external HD.
Are you saying I need to reimport the entire contents (all the music) in my iTunes Media folder?
I thought your solution was aiming to simply rebuild the directory structure while leaving the original music media alone.
Thanks for helping clarify.
Or could you point me to a support.apple.com/kb article?

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Random iTunes library problem or bug with duplicates

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