There isn't going to be any way "not to read" the smaller pulses because you have to read them in order to know that they're small -- it's a catch 22. Thus, you're only option is to detect whether the pulse is large or small and execute different code accordingly. With the existing case structure in your VI, simply put "large pulse only" code in the TRUE case, "small pulse only" code in the FALSE case, and code that applies to both cases
outside the case structure. Following this organization should ensure that all the code is executed at the proper times.
Kind Regards,
E. Sulzer
Applications Engineer
National Instruments