I have suffered these problems. And worse (you are maybe also suffering them but don't know it... yet)
More Specifically:
1 - Tracks linked to wrong files in itunes (can't update them in any way, thanks Apple), in some cases they link to the wrong MP3, in others they link to an album or artis folder (argh!) and itunes doesn't even see the difference.
2 - Itunes changed the names of tracks and moved them to wrong folders. When you play them in itunes another track plays instead.
I.e. you play Help by the Beatles, and you get "woman i love" by Barbra Streisand, but the file shown in the finder resides in the Beatles/Help folder, and is titled Help.mp3. Interestingly, when you play it in VLC the metadata displays correctly Barbra Streisand... The bad thing is that when you rename the file to "Woman in Love" put it in the right folder (under Barbra Streisand) and import it again, itunes shows it as "Help" by The Beatles until you actually locate it in itunes, double click on it and Bam: it transforms itself to Woman in Love (with album art and all). Duh?
3 - Complete folders relocated as tracks in another artist/album folder.
For instance I was missing all my Duke Ellington (22 albums) and after long searches I eventually found that the track "Back In Black" by ACDC had become a folder aptly called "Back in Black" and within it I could find all my Elington Albums. Unfortunatley these included a few tracks affected by problem 2 that would not import correctly. The file BackinBlack.mp3 is lost forever. In the itunes library the track Back in Black does not play, but itunes doesn't see the difference (duh?).
I managed to export the XML library to excel to analyse it: 58885 tracks... after running a few routines for the most obvious consistency checks (file name to song name, artist in path to artist in XML tag etc) I found that I had:
a - 33 tracks that were turned into folders (case 3). When exploring these in the library I could see that these led to a lump amount of 127 album folders, whose location was lost in the itunes library. That's 127 albums that itunes lost without noticing it!
b - 355 tracks misplaced (whereas they were moved into the wrong location) - randomly testing some of them I found that a few did not play the matching song (case 2 above). But they retain the appropriate MP3 tags. The others simply need to be imported again.
Unfortunately Excel doesn't give me the tools to check the consistency between track name and the actual music it plays, but for the rest it gave quite a solid appreciation of the terrible job itunes is doing. I wish I could extract the MP3 tags from the files to compare them with Itunes library information and run the last consistency checks.
While cases 1 and 3 are quite 'easy' to spot (but long to manually correct), I don't see any way to systematically track cases 2. Any help would be appreciated.
Now, all this happened for one single reason: I am hosting my music library on a NAS and obviously itunes hates this, but when your library reaches the size of 400 Gb, how can you consider keeping it local? I cannot express how angry this is making me. I don't see any solution to correct this, unless there is a way to reimport everything forcing itunes to read the MP3 tags, and not the itunes data it has embedded in the file. I can't even start to imagine how long this would take (on a network drives things can be quite slow...) and I wonder if itunes would be able to handle that at all! Frankly, after what I saw in the xml file... I doubt it.