Easterhay said:
Because the disc on which Yub Nub appears is a disc of extras, combining cues from all three films. The ESB take is the one from the film, not the one released on the album, hence its inclusion on disc four.
But why combine it with the ROTJ ewok/celebration music? Just to be able to squeeze both unreleased pieces onto the disc? (In which case I've answered my own question). ;-)