The data file posted on pastebin contains data from two channels recorded during the same measurement. 2nd col. vs. 1st col. is one dataset and 3rd vs. 1st. is the other.
in reply to Re^3: Finding local maxima/minima in noisy, pediodic data
in thread Finding local maxima/minima in noisy, pediodic data
So you are plotting the right values.
You are also correct about misses and false hits.
Anyway, here is your first graph with missed peaks marked with ugly blue arrows and false peaks marked with smaller but equally ugly gray arrows.