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L+R is mono with left and right channels averaged together. Stereo is two channels processed independently.
I tried with 250hz pure tone (I created with audacity) and your app worked just fine when assigning harmonics. Strange that using pma pure 1khz tone could cause such differences.
Anyway, is there a reason why using "L+R” option to save files would create files that sound much better than saving using “stereo”?
L+R is mono with left and right channels averaged together. Stereo is two channels processed independently.