I'm not familiar with the Haltech, but do you know if it gives you a screen shot of the sync and reference signals? I know the motec does this and it helps to show how close your sync and ref signal falling edges are to each other.

I have had issues with the falling edge of the sync signal being too close to a falling edge of the reference signal. So basically the tooth on the cam lined up with a tooth on the crank. It would synchronise on cranking (<600 rpm) and provide fuel/spark but as soon as the engine went faster the signals would overlap and it lost which tooth was the reference to TDC and die.

It might be worth changing your sync signal to rising edge, leave the other as falling edge and adjust your crip (In motec terminology) to see if that makes any difference.

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