To reconfirm - the VR conditioning circuit (standard V3 type) was behaving perfectly, not conditioning problems at all. However the input signal from the VR varied from textbook perfect to... absent...
Top trace. Input to CPU.
Bottom trace input to Megasquirt board.
Note1. For some reason my software is showing the signals upside down.
Note2 - the inputs I was using here are capacitively coupled, so at low revs the digital top trace gets a bit messy. At higher rpms it is nice and square.
What you can see is that even with low input amplitude the V3 VR circuit is working fine. However, then my VR sensor or wiring decides not to input any signal at all.
bad vr signal2.JPG
There seems to be some myth about hall sensors being immune to noise. The noise isn't usually the sensor itself, but in the cables from the sensor to the ECU. The noise energy doesn't care what sensor is attached to the other end. Say if your sensor cables run parallel to the high tension spark plug wires you'll almost certainly get a problem.
James