How are the batteries wired? The charge / load cabling should be split in such a way that all the positive cables should be wired to one battery, and the negatives to the other. This ensures even charge and discharge across both batteries (very common mistake to have everything wired off one battery). If my suspicions are correct, the "problem" battery would have been the one with nothing wired to it (except the cables from one battery to the other). Please fell free to call me on 08 8322 4848 to discuss if required.