This is what I've worked out so far:
The trigger log shows that when the engine starts to fire, two things happen;
One is the primary trigger signal line shrinks down to a small length.
Why is this? What does the length of the trigger line represent?
Two is there appears another very, very short primary trigger signal line about 3ms after the correctly placed one. This equates to the sudden jump from 300 to 5000 rpm that is seen in the VEMS log which causes the sec errors and crazy fueling (5000 rpm worth of fuel at 300 rpm = violence).
What could this extra signal be? As my config uses Rising edge, it looks like it could be the Falling edge of the signal. Is this possible?