I think you should be using Rising Edge for your Ref Sensor Edge Polarity. This will require changing your CrIP value.
It's unlikely that is your problem however.
From the Ref/Sync capture, there is some timing differences in the sync signal between two subsequent cycles (sync falling edge @ t=0.01224 and t=1.0872 and t=2.0502) -- it looks to me like it moves about 1deg-- you might want to check the chain tensioners on that engine !
I suspect you have an intermittent connection in the sync sensor wiring. Wire broken at a terminal crimp either at the ECU or sensor end. Sync Error is most likely a dropping of the Sync signal which looks like an extra sync pulse.
BTW - there is a hole in your fuel map, 2000 RPM / 60 % throttle, 18 probably wants to be 68