For the 2004 Editions the Vader lines from the OT were all "re-modulated" or "cleaned up" to sound the same. Not sure if the 97 line addition was also cleaned up or not, but it clashes at least with how we "know" Vader's voice in ESB proper.

This might explain the difference. And yes, that's JEJ in Episode III. The only part that isn't, supposedly, is where he says "Yes Master," (after "can you hear me," as featured in all those trailers before the movie came out) which is supposed to be Hayden Christiansen's voice heavily modified (ironically, it sounded to me more like Liam Neeson, who of course had his "force voice over" modified in Episode II.. where he says "Anakin, Anakin" which is from Episode I, and then "Nooooo!" which is somebody else trying to do an impression of his voice).