Something has changed, surprise, surprise!
It is the reduced aliasing.
And this fact by nature of things changes the spectrum slightly.
If you need 100% identical spectrum analysis, you need to compare identical sounds.
Again: Anti-Aliasing slightly changes the spectrum, otherwise this would be proof of
no anti-aliasing taking place.
BTW: Same happens in image editing and can easily be measured in Standard Deviation or Median Deviation,
even if you can't tell the difference between two images visually.
Just my 2 cents,