Itunes duplicates and removes songs

Hello all!
I'm having some problems with iTunes for a while now. I'd like to use the feature that all my imported songs are automatically positioned in the iTunes folder i've specified and that iTunes then renames those files and neatly puts them in folders. This seems to work just fine.
However, although I know for sure I have not been importing new music for a while now, sudden duplicate songs keep popping up. Complete albums will duplicate itself and I keep spending time to remove those additional songs. They keep coming back!
Simoultaneously I've noticed that from some albums that are still intact on my iPod (I sync manually...) suddenly some songs seem to dissapear! For example on some albums I'd suddenly miss song 3, 6, 7, 9 and 11 out of 13.
Does anybody else notice the same problems? It doesn't seem safe to use iTunes at all to organize my music collection...

Rule 1. Backup, then if something truly goes missing you can fetch it back again.
Rule 2. Don't ignore Rule 1.
iTunes doesn't appear to do any reorganizing of tracks except when you actively edit tags or, if some third party tool has made a change, when it has cause to read the data, say during playback. If a file is removed from the drive iTunes should retain an entry to it which it will flag up with an exclamation mark if it ties to access the track. Likewise iTunes doesn't scan your drives for new tracks so duplicates should only be generated if you actively reimport the same content.
To make sure Windows Media Player is leaving your content alone take a look at this post.
For help with duplicates see my DeDuper script and this thread for background on it.
tt2

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