To specify, the pitch gets wonky on the first melodic phrase after you introduce the first 4 chords. It’s the second note of the melody E A B… A is not tempered at 440hz to the scale!
I'm not sure we're looking at the same thing, but I fixed an issue with the just intonation transcription. Now, the largest non-transient deviation from 440 Hz scale is 0.14 semitones, caused by Debussy modulating by a third (5/4).