ITunes creates duplicate entries

Hi.
I noticed that if I transfer a song to my iPhone, and later add lyrics or a cover (or even give a rate) to that song on my Mac, if I transfer the same song again to the iPhone, iTunes instead of updating the infos of the already existing song, creates a duplicate on the iPhone, that differs from the old one just for the detail I added later on the Mac.
Is that a known issue? Am I the only one experiencing this problem? How can I fix it?

I'm not really sure how unchecked tracks behave if they are synced to the device. I only uncheck things I really don't want to hear as a rule but don't actually want to throw away. E.g. interview tracks on an album. In the main library unchecked tracks will be skipped unless you specifically click on them to play them. Presumably it works the same way on the device, I've just never tested it.
tt2

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    http://dougscripts.com/itunes/itinfo/dupin.php (commercial)
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    I decided to change the advanced preferences in iTunes to an entirely new folder on the External hard drive.  Then I could just go back into File -> Library -> Organize library and select only the "Reorganize files..." checkbox without selecting the "Consolidate files" checkbox.  I figured this would just move all the files that are in the iTunes dB to the new iTunes folder.  Ummm.... but no.  Apparently this "Reorganize files" checkbox is only available if you select "Consolidate files"...?   To be clear, "Reorganize files" is greyed out.
    So to summarize:
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    2.  What is the right (and I pray easy) way to get my library back to the right size and consolidated into one place?   I'm still dangerously low on disk space on the mac...
    <sigh>
    Thanks for reading through all this! 
    Tim
    Mac Mini  OSX 10.8.3; iTunes 11.0.2 (26)

    See this thread for background on why iTunes can end up with duplicates and how they can be systematically removed. The script there is for Windows users and the "show duplicates" menus have moved around in iTunes 11,  but the advice on clearing recently made duplicates should still hold.
    As given in my older post "Reorganize library" is meant as a one time command to change the structure of a pre-iTunes 9 library into the newer layout that places music in its own subfolder of the media folder. Once used, if the option becomes available again that suggests that a file called .iTunes Preferences.plist in the media folder has been deleted or editied.
    See also this post.
    tt2

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