I reviewed my setting compared to yours. Under "Ignition Options/Wheeled Decoder" I have "Ignition Input Capture" set to falling edge. The note shows this setting will correct timing drift. I do recall checking to make sure my timing was stable under varying RPMs with the timing fixed. I'm thinking falling edge may be the default because I don't remember having to change this to correct instability. I'd be interested to hear what others have theirs set to on their MS3.
I see their note says it was a mis-fire cut out. What was the timing doing during the cutout? Was it stable? If it was, the computer is doing its job and I'd look for a hardware issue. Plug wire, spark plug, coil, etc. Have you put a heat gun on each of the header tubes to make sure they are similar?
