I have noticed a lot of issues with the sound on the 2004 SE version. The new additions have musical edits that aren't always very smooth.
Also with all of the prequels, the music was scored before Lucas was done editing them, so there was a lot of patchy editing going on there too, with AOTC and ROTS both re-using music from previous episodes, something that had never been done up until those 2 films.
I am thinking that Lucas is going to re-score the films with Williams once he's settled on a final cut.
I know it's not "final" until Lucas can't change it anymore, but I think Lucas is trying to reach the finish goal.