If the batteries are not each at the same voltage this means that one battery is charging higher than the rest and one is not charging as high as the rest. Charge more than five batteries by connecting one 12 volt battery charger across each battery in the series as if each battery were the only one being charged.

12v Battery Charger Circuit
Charging two 12 volt batteries in series. To charge two 12 volt batteries in series youd need a 24 volt charger. Charge all the batteries at the same time. This requires only one bank of a 12v charger to be attached to the positive terminal of the first battery and the negative terminal of the second battery. Charging only some of the batteries will result in batteries attempting to equal out the power and charging each other. Two 12 volt batteries wired in series produce 24 volts but the capacity remains the same as one for a 12 volt battery. In basic form here is the difference between wiring two 12 volt batteries in series versus in parallel.
Thats the pat answer. In the second example to charge a 24v system simply use each bank of the charger on each 12v battery terminal leads. You need to overcome the total voltage of the series batteries 12 v 12 v 24 v to drive electrons. The basic concept when connecting in series is that you add the voltages of the batteries together but the amp hour capacity remains the same. When you charge batteries in series you are charging the entire group of them all at the same time. Two 12 volt batteries wired in parallel continue to produce 12 volts but the capacity doubles.
As in the diagram above two 6 volt 45 ah batteries wired in series are capable of providing 12 volts 6 volts 6 volts and 45 amp hours. The parallel circuit still generates 12 volts but doubles the amperage output. Batteries may be wired in parallel or in series. The charger will stop charging when the entire group reaches a certain voltage. Charging 12 volt batteries wired in parallel requires a 12 volt battery charger. In the examples below two 6v batteries in series 12v.