Did you ever find the problem? I have just bought a NGT and that do the same. If I connect the charger direct to one of the batteries it do the same as yours. If I charge through the bike or via the split box it works.
And then I have another problem on top of that, it takes forever to charge the batteries. From 30% to full it can take 20 hours. Half that time if I disconnect one battery and charge one, so it seems that the charger cannot deliver full power…