I'm almost positive that the missing treasure chests is a bug caused by the 1.2 patch. I've e-mailed Bethesda support, but so far not response. I easily found treasure chest #1 when I played the game originally, but then I started a new game with the 1.2 patch, and no treasure chest where it was supposed to be. I've read of other spawning problems with the 1.2 patch. I hope they fix this soon; a typical "patch" that breaks more than it fixes. I won't be playing the game until they do something about this.