The Academy instituted a rule awhile back (I believe when the second and third Back to the Future films were shot simultaneously) that if the nominating committee feels that nominated work for films that were shot at the same time but released in different years was not substantially or significantly different from each other, then it could chose not to nominate the work after the first time.
I believe that is why TTT and RotK were not nominated for cinematography after FotR won, and why TTT wasn't nominated for original score.