Check battery connections.
After driving see if any are warm.
Rodney says “bright and tight”.
If you have a peak reading meter, leave it connected across battery string during a charge cycle.
A bad battery connection, internal or external, will cause voltage to spike.
While you are checking, read the flashes when first powered to see what profile is being used.
Check each battery voltage. You will probably find 1 battery with significantly higher voltage than the rest. This battery will probably discharge faster than the rest. (more common with AGM’s) You might think about replacing that battery down the road.
Are you sure you have the right algorithm programmed for your battery type?
Good question.
I’ve never seen a charger do that. Yet I don’t know how batteries could be the cause.
A charger is easier to try than batteries.
Do you have access to another charger? Even in another car.
I wonder if it can be temperature related. Is the sensor connected?