E&A strings reversed..

[Ken Smith]

It's not just the length change when switching, it's also the angle of pull. The A-string is now a much sharper bend and the 'E' is shallower than before. Considering the thickness of the E-string (.105 avg) combined with the normal sharp angle pull, the switching to the upper peg is a drastic change. Perhaps the 'freedom' given to the string when moving it to the A-peg reflects back in the sound and tension as well.