Ref/sync gone lost during engine run

[MaBaMM]

Hi Members,

today we would run the engine (Honda CBR 600 RR PC40) after rebuild the whole car and engine.
Everything is done. All sensors and actuators are OK. The settings on our M800 is the same like a few weeks ago as we were testing a running engine/car on track.

After a few cranks the engine starts running @ 1500 - 4500 rpm with idle throttle position (maybe a little bit more, hands on)
So, after a minute the engine doesnt stabilised how we expected. We drive this engine since 10 year (we buy every season 3 or 4 new engines, but the same model) So we just now the sound and enything else how it have to be.
Today it wasnt like that.

The engine runs up to 4500 and then fell down to 1500 during a minute.
Yes, the engine is cold, but we have the same engine on the dyno. And there we couldnt notice such a behavior at any time.
So the engine will run at higher rpm like 4500 - 5000 for a longer time than just a few seconds, but it cant.

After a few tries we noticed, that the ref/sync get lost during runing and after a second it found it again. and so on.

How can the ref/sync get lost during running?

We also measured a capture and there is everything fine. (see second pic)
We have a magnetic sensor for ref and sync.

We have checked injectors and ignition, the firing order, MAP, BAP, Fuel Pressure, Oil Pressure, Temperatures and so on. No compensations are active or just on low levels. No Speed Limit. Oil level ist a bit above minimum.

We also have a M150 wich we would use as our primary ECU. But today we would run the engine with the M800 at first to ensure that we have done everything right.
With the M150 we also have measured a capture and there is also everything ok. (see first pic)

While we run the engine i noticed that the generator, wich is charging the starter battery during engine cranking and running, doesnt load any more. Normaly it does. Also the Battery Voltage was at 12V and not at 14.7V.

Is it possible that the engine doesnt get enough voltage to charge the ignition plugs?
We also take off the alternator from the engine.

Next tests will be done at monday cause in bavaria is vacation time.
So more time to set up a test shedule.

I know a bit to much text, but i would explain it very detailed for you.

Thanks for any help
Greetings from munich
Malik