I'm on 10.7 of iTunes now on a MacMini mid-2011 + a MacBook Pro mid-2009. I turn on Home Sharing to access one iTunes' content from the other, and both are authorized to the same Apple ID for the iTunes store.
I've been using iTunes since it was first released and have a fair amount of old data.
I have the content stored on an external HD for the Mac Mini. It is defined in the iTunes > Preferences > Advanced tab as "/Volumes/<HD Name>/iTunes".
Keep iTunes Media folder organized and Copy files to iTunes Media folder when adding to library are both checked on.
Within the "iTunes" folder on this external drive, I have an "iTunes Media" folder, but it also contains the older file structure folders here as well: "Album Artwork", " "Books", "Movies", "Podcasts", "TV Shows", etc. etc.. These folders also all exist inside the iTunes Media folder. Sometimes when I use the File > Add to Library... option or even when I drag and drop something like a movie into the iTunes main window, it will get copied to the iTunes > Movies folder, but sometimes it will be copied to the iTunes > iTunes Media > Movies folder. Sometimes it will get copied to both.
When I look at the item in the iTunes window and command-I or File > Get Info on it, it will point to the iTunes > iTunes Media > Movies folder, but when I browse through the folders in the Finder or the Terminal, I can clearly see the movie file does not exist in that folder, it exists in the iTunes > Movies folder instead. I can still view the content and watch the movie, it is only that the Get Info dialogue box is incorrect.
All of this seems to result in the odd behavior I experience - one day I'll add new content to iTunes and the next day it has disappeared (from the iTunes window, not from the computer itself). I also end up with lots of duplicated content on the drive.
When I access the File > Library > Organize Library menu option, I have the ability to select "Consolidate files" but not "Reorganize files". If I try "Consolidate files" the window pops up with the progress indicating it is moving data around, but it disappears after two seconds and nothing has changed.
Clearly my iTunes is using both file structures and is getting confused about it, but I don't know the best way to fix the problem. I'm worried about manually renaming folders or trying to rebuild my Library as it is probably confused anyway.
Has anyone else seen this kind of behavior?