The story I've heard about the separations is that they were incorrectly made back in 1977 and one of the three channels was duplicated in place of the third channel, or that one of the three was found to be missing when they were pulled for the SE restoration.

(And this isn't the only time I have heard of this happening; when Disney restored Pollyanna in the late 90s/early 00s, they were working from a faded original negative, and when they pulled the B&W separations out of the archive they found that they had only two of them, with the third being a duplicate of one of the other two.)