Hello Luke and thank you for the post.
Could you post the captured waveform here so I can take a look at the raw signal?
Rather than using the frequency coupling feature, just measure the digital output (DC coupled)
Could you let me know the version of software you are using at present?
One more question (sorry) could you let me know the vehicle under test? (Manufacturer, Model, Year, Engine code etc)
Why I ask is that I have seen a number of vehicles with possible additional information contained within the digital MAF signal. (Peugeot)
The frequency coupling feature "crossing points" may need amending and I can experiment with these for you if you can help with the request above.
A maths channel or a "current" measurement may be alternative options
I hope this helps, take care.......Steve