In my case, I believe I understand the issue and it is entirely up to Apple to resolve it. Because most households now contain more than one computer running iTunes and because it is now relatively common to use network shared drives like Airport Extreme 3TB, it's not unheard of to have multiple computers accessing the same set of library files through a network shared drive (rather than through Home Sharing).
It seems that when two (or more) computers are running iTunes against the same set of library files (music, movies, etc), each computer's iTunes software is battling over who has last updated the files. This is especially a problem if one of the computers is running Windows and one is running Mac against the same set of media files.
It doesn't make sense to have two or three copies of your music files in different folders when you can share the same set across multiple computers each running iTunes. However, it also appears that it is now no longer safe to run multiple iTunes instances on multiple computers using the same set of media files. It seems that to solve this problem it requires duplicating your library once for each installed iTunes instance so that each instance has exclusive access to the files.
Note, I found this out because my Mac had been the exclusive owner of the media files for a month or so. After I launched Windows iTunes against that same set of files, all of my files needed to be synced again to my iPod. This means that each iTunes instance is scanning and modifying each of the library files for some reason. This is at least the cause for my issue. It may be the cause for others here.
The only way to fix this problem is to make sure that the media files that are referenced in your iTunes library have exclusive access to a single instance of iTunes. No other iTunes software should access those files or you risk having the resync everything problem.