Dave Mack pointed out that the FFT amplitudes of 3h09bY was smaller than 3h09bX which implied maybe I had the signals mixed up. But I was using the signals seperately. The actual reason was that we still don't have that 4mm electronic offset for 3h09bx going in to the analyzer and that caused the magnitude of 3h09bx FFT to be huge. I temporarily add the offset by hand in the FFT script for 3h09bX and here is the new FFT results I got. Now we can clearly see what we expected to see : Both signals got 60Hz in them but 60Hz in 3h09bY is about 5 times bigger than in 3h09bX.
Figure 1: FFT results for 3H09BX run 6251
Figure 2 : FFT results for 3H09BY run 6251
