#5398, "RE: MSII Help, Losing Sync Randomly" In response to In response to 0
What type of harness are you using? Is your crank sensor signal shielded? By changing the MS grounds to the battery and leaving sensor grounds to wherever they are, you are offsetting your ground plane. For the cleanest signals, you should ground all input sensors for the MS to the same point as the MS grounds.
Also, in the future, post your MSQ and a datalog for people to help you diagnose, otherwise our guess is as good as yours.
Capture the crank signal as well using TunerStudios and post it up.