Here is my theory...
Keep in mind I'm a mix engineer on a mastering forum.
The mixes are fine. The fans are complaining the Playstation version sounds fine but the cd is awful...
Metallica "Death Magnetic" sounds better in Guitar Hero - Mastering Media Blog Fans Complain After “Death Magnetic” Sounds Better On “Guitar Hero” Than CD : Rolling Stone : Rock and Roll Daily
The mastering engineer did as he was told. Make it louder, louder, louder. Jensen doesn't want to blame Rubin or the label because he doesn't want to lose a good gig (to late).
Theory #2. they made a "special version" to give to "the drummer guy" to shut him up. Then accidentally sent the wrong version to the plant.
The loudness wars are over and Rubin won. Unless they can figure out how to get rid of that annoying silence between the songs.