If I managed to find a second hand mav.2 on .0670 firmware: I'd snap the sellers hand off. Last fully featured firmware on ARB#1 without all the subsequent "security fixes".
Great! That confirms no problem with any of the new batteries, and insufficient power on the hub charger to function properly. You need at least a 30W charger. Double check by charging the third battery in the drone, too.
Except in the video, neither battery is charging. Both are flashing the low power input flash on LED 3 because the OP states he is only using a 20W charger, instead of the minimum of 30W. That's the real problem.
This is precisely what is occurring. The battery with the highest charge level is first topped up, followed by the other two in turn, prioritized by the charge level detected in each one, until all three are fully charged in sequence.
One thing it could be. The DJI charger charges one battery at a time, starting with the battery with the highest remaining charge. That enables the quickest time to get a battery fully charged and the drone back in the air.