Sounds like the software was not communicating with the scope. You won't have the frequency select in the coupling dropdown unless the right scope is plugged in and communicating.
Just suggestion here though..
There is no reason I can think of why you would now ever want to graph frequency live. Why waste the channel? Use your channels to capture the MAF voltage and three other inputs. Then later, apply a frequency math channel to the desired channel. This can be done with a saved capture and the scope doesn't even have to be there.