IIRC, and I may not, the music during the Naboo scene is just a generic percussion section and it was just looped for another three seconds or however long the shot is. That entire section just has a generic tamborine/drums/percussion section to it, and then the flute melody comes in only after the camera pans up to the sky at the end of Coruscant and it dissolves back to Endor.

Also, there should be some frame differences between the GOUT/pre-SE and the SE due to cutting the negative. You can see that on shots that come before or after an SE change it looks like there is a frame or two missing. Star Wars was an A/B roll negative though, which means the negatives are checker-boarded and filled in with leader and then printed together, so I'm not sure if it should be affected this way.