I bet the "better" audio is "less pure" from a flat frequency response stand point

No, if that's the case then it's a bug - but I don't believe it to be the case. Karma also has a flat response when the EQ is set flat.

I did notice that my "Loudness" setting was active after loading -alpha5 however I don't know if this was operator error or a bug in parsing the older settings data.

Rob