"To my surprise, in the rock examples the MP3 at 128 was preferred. I repeated the experiment over 6 years and found the preference for MP3 - particularly in music with high energy (cymbal crashes, brass hits, etc) rising over time."

Encoding to MP3 @ 128Kbs will apply a low pass filter (so that more bits can be used to encode the lower frequencies) and high freqeuncy sounds can sound smeared. I would guess one or both of these factors could be responsible for reducing harsh sounding treble.

I'm guessing of course but if right, I wouldn't say the MP3 was better. Merely, it masks a horrible sound to begin with.