I have seen this several times with the minn kota chargers. If the batterys drop below 12 volts the minn kota charger cant bring them back up. Try putting a regular trickle charger on them for a little while then plug the minn kota charger back in and see if that works.
That is correct with just about any of the new chargers, if one of those batteries is dead it won't charge it. It has to have a little charge already in it for them to charge.