ITunes not removing files duplicate files or organizing properly

I have iTunes set to keep my files organized (i.e. in directories matching the albums and artist names) but recently it stopped doing this properly. Also I spent a lot of time deleting duplicates and clicked to remove from hard drive as well but in many case it didn't remove he duplicates. I don't know why.
I want to back up my whole library but i want to make sure it's "clean" first.
Is there any way to fix this problem?
Maybe the easiest way is to make a copy of all the MP3 files and just delete the whole iTunes library and rebuild it, then go through and delete the duplicates again. Would this work? Is this safe? Does anyone have instructions on how to do this?
Thanks.

My problem is not related to that other thread, however it appears the same thing that's causing this problem is causing the problem with the ID3 tags so there is no need to discuss in two separate threads. Thanks.
http://discussions.apple.com/thread.jspa?messageID=9304233#9304233

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ITunes not removing files duplicate files or organizing properly

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