Phasing? I can't say I've noticed anything like that, but then I haven't had any formal training in this sort of thing, and my sound system probably doesn't really measure up to professional standards. Do you mean something goes wrong briefly at specific points, or is it a more long lasting issue?

The only main channel edits I made to ESB were to insert a small segment of the 1980 stereo mix into the '93 to put back the missing snowspeeder crash sound, a splice from the '95 Faces audio when the Falcon attacks the Avenger to remove a high frequency glitch in the left channel, and a tiny segment of the GOUT audio to fix the weird music jump at the beginning of the carbon freeze scene. The alternate version also uses the '97 mix for Boba Fett's departure from Bespin in order to include the unedited music cue as heard in the SE, but that's not on the disc you watched. I made sure each of these edits was sample accurate and maintained the proper phase, so aside from a possible shift in imaging or EQ I can't think why there would be any issues, unless something about the upmix is making it sound less than ideal, or if the bass isn't quite synched perfectly.

I hope you enjoyed it apart from that, anyway. ;)