What was the current coming out of the charger? I am assuming the older batteries were taking too much current and holding the overall voltage down.

Were the charging leads or any battery terminals warm? This could tell you which ones or if the charger was taking excess current.

Another thing that can cause uneven charging or even damage batteries eventually is connecting the charging leads to one end of the bank then daisy chaining the rest of the batteries to the end. The charge leads should be connected pos on one end and ground on the opposite end to keep resistance and voltage even to each battery.