There may be a bug in the comparison VI. I experimented with simple waveforms (0,0,1,0,0) and (0,0,1,0,0,1). I used the greater than with a cut off of .5. I also set the VI to output one answer for the entire sample.
I saw that the VI outputed 0 for both data sets. When I used the property page to invert the input, both sets outputed 1. I believe that if you just inverted the output of the comparison VI, you will be fine.
