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I have never used "bar" frets. I am thinking that that may be where your difference lies.
I love it when those happy accidents happen!
David

My money is on the bar frets. Those necks feel different. They're heavier, and with the kind of contact the frets have with the fretboard, I'd bet the mass of the neck has a closer acoustic coupling between the string and the fretboard. It might also be stiffer( because of that manner of contact between the fret and fretboard), which would definitely have an effect. Grant, you've built with bar frets before. Did you notice a difference in those guitars?

Does it have the neck stiffener setup? I've found that old t-bar Martins sound different up the neck compared to those with truss rods.

One thing you could do with the necks off is to compare their resonant frequencies. Dangle the neck from the nut end where the neck width flares out from the shaft to the headstock and tap at various places along the neck. The resonant frequency will be the loudest low one, and compare it with another neck. Not conclusive, but provides more questions for the guessing game.

Pat