Well, nevermind. Apparently when I ran it through Handbrake, it converted the audio to Prologic II. The source audio sounds fine.
I don’t see why that would make it sound weird though, almost any stereo source for a movie you’ll find, and any official source for a star wars movie that is 2.0, is going to be matrix surround compatible. I mean that would mean the 93 laserdisc mix would have sounded weird if played in stereo.
Given that it into happens at those moments is a pretty strong indicator that it isn’t related to the pro logic encoding… I’ve downmixed a ton of 5.1 sources to pl2 2.0 using handbrake and they all sound fine in stereo.
However I have had downmixed done with avidemux have that issue. Maybe you’re using an outdated version of handbrake that has a different script for it?