Have the two batteries in your 24volt configuration load tested, mise-well check all three. I bet you have a bad battery. And no need to disconnect the batteries (jumper) to charge them individually when connected in a series. A little more info would help as well, like the size of the boat, group size of the batteries and if you have had problems in the past before the interstates pulling cranks.

Could be a bad bank on the charger as well, charge them up full and use a multi-meter to check voltage on them after they have cooled for an hour or two.