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The calculated goodput should always be less than or equal to the measured throughput; if not, then there's probably a bug somewhere.

Throughput is just the amount of data per measured time. Units can vary but are typically bps (bits per second) or Bps (Bytes per second), or some multiple thereof (Kilo, Mega, Giga, Tera, …).

I assume the MA Window means the Measurement Analysis Window. It simply sets the time window over which the measurements are taken and graphed. The default is a 1 second window. The larger the window, the "smoother" the graph will be because you're basically averaging the data over a much longer time period. Conversely, the smaller the window, the "rougher" the graph will be because the data is being averaged over a much smaller time period.