What you've just found is a feature of the data acquisition system (DAS). The DAS scans all of the instruments at 20 Hz. A cup sends a pulse each time it completes a part of a rotation. So, if the wind speed is too low, we won't get any pulses in a 1/20th second interval and so we don't have a wind speed measurement. But, to keep the data files simple, we record the previous measurement in the data file. This approach is not uncommon, especially on a complex system. You get a hint of this if you look more closely at your data plot; on the right hand side of the plot you'll see that there are 14 M5 measurements that are the same, rather than 20. This trick of repeating the previous data reduces the amount of energy in the higher frequency part of the power spectra of the turbulence (you could think of it as being a low-pass filter). You should be able to see a plot below from a randomly-selected data file that shows how the M4 and M5 cups can vary.
At this point it's worth me reminding all users that
the sonic anemometers are the primary measurements for speed on the tower. The sonics have no moving parts, no inertia, and no issues of frequency or gust response. The cups, on the other hand, have a very odd frequency response and show a dependency on the previous measurement, and get confused in upflows, and they are closer to the tower body.
If you are interested in learning some more about this, try plotting out the power spectra from the sonics and cups. You'll see that both follow the typical -5/3 decay curve for a turbulence measurement, but the cups show a much higher noise floor (where power is not a function of frequency). Importantly, the higher frequency range does not contain much energy so that noise does not impact the variance or the turbulence intensity. If you were going to use higher-order moments from the data (i.e. not just the mean and standard deviation, but also skew and kurtosis) I would recommend using the sonics.
Hope that helps? I'll try to get this written up in the documentation.

- Clifton_NREL_M4M5Comparison.png (12.43 KiB) Viewed 9140 times
Andy Clifton, Ph.D.
Senior Engineer