For anyone else playing along re timing issue.
A good unbiased thread here.
Unsurprisingly issues occurs on a number of ECUs, not limited to Haltech, and even features our OP(and others) claiming the same issue on a PowerFC, madness...
Seems like most ECU manufacturers and Tuners were aware of and had produces solutions to address it, including modified/better CAS discs, crank triggers, etc.
Too much was said for me to not look into it as a precaution - So thanks for that even if your caps are flat.