The positive duty cycle scalar measurement should correctly calculate duty cycle on your pulse. By default, the measurement finds the base and top of your waveform using a histogram of the Y values (there will be peaks in the histogram at the base and top values). Duty cycle is calculated from the 50% level crossings between these two values. You must have at least one complete cycle and only the first cycle is measured.
If that doesn't work for you, there are a plethora of parameters you can change (except for which pulse you measure - it is always the first). For example, you can set the upper, lower, and level crossing values to specific % or voltage levels. See the documentation and examples for details.
If you need to measure the duty cycle of multiple pulses in the same pulse train, there is a LabVIEW function (Pulse Measurements.vi) which allows you to do this. It uses the same algorithms as the internal NI-SCOPE routines.
In either case, the measurement is independent of the hardware. Any NI-SCOPE device will work. If you have any other questions, let us know.