I have the same type Mickey Mouse setup on mine. Indicator lights on the range vent hood. If and when the batteries are at 12.6+ it will show full charge, if it drops below that 12.5+ it will show fair. If the batteries are being charged from any source (motor/converter) pushing the button lights them all.
Fresh water and Grey water tanks indicators are reasonable, but the indicators for the black tank are ridiculous in their indications.
As for the battery indicator lights well they are just that, indicators, go by what your meter reads. Depending on how far the batteries are from the panel, there could be a loss in the wire causing your problem.