I tried out the auido diffmaker, and it seems to be a pretty good program. If you check the help in one of the final chapters it makes mention that it best works if the DAC and ADC have the same clock. It does not account for dynamic variations of the sample frequency. Provided you look data over shorter periods and at the lower frequency ranges, this is not too much of a limitation. So the null that was found is likely the point where the waveforms were time correlated. If you estimate a difference of about 0.001 ppm between two recordings from the same source, that would be extremely good. I would not be surprised to see a variation of 1ppm of the same oscillator over time: even more just during warm up. I tried audio diffmaker to compare the output of an ipod to a toshiba laptop using the supplied pink noise burst. The plot is of the resulting Audio DiffMaker output.
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