Also, read into how PWM works before you spend too much time measuring the output voltage. You'll need to use either an oscilloscope or a resistor-capacitor low pass circuit. That should make sense once you get a good understanding of how those things work.
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I read up a little on PWM. I probably have more questions now than answers, but it seems what you're saying is although it shows lower output than the input current, this is false information? I don't have an oscilloscope but seat of the pants airflow with/without the DC controller seemed lower with. I'll have to buy something that actually measures airflow to know for sure.