Hi,
We think we may have fixed it.
The problem appeared to be that the sensing element of the sensor was too large pick up only a single tooth.
Therefore the rising edge of one tooth would be cancelled out by the falling edge of another producing a rather odd waveform, and also reducing the amplitude of the majority of the signal (all apart from the missing teeth area).
What we had been looking for in the waveform was more the symptom rather than the cause. Another team at FSG told us that they had similar issues and fixed the problem by making the end of the stock sensor smaller by machining it down to about 1mm wide. Thanks to the guys at CAT Racing!
We're not certain its worked yet; a track test is needed yet to be sure, but it revved freely to 14000 rpm on the stands even with quick throttle application. We haven't been able to do that for a while....Fingers Crossed.