Understood. Since we are already having trouble with the TOF calculation this might not help, but you could use the absolute times of flight and compare to the oscilloscope capture to see if the reported absolute times are corresponding to the start of signal 1 or 2, which would help shed some light on which signal is actually being used. Noted about needing to continue using the V setup. If your continued testing reaffirms that the signal 1 and 2 are interfering and "confusing" the algorithm, maybe another hardware change that could help is adjusting the angle of the V so that the gap between the 1st signal ending and the 2nd signal arriving is greater? Then you could adjust the ADC capture window to only collect one of the signals.
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