I don't profess to be an expert on batteries, battery types, and recharging. However, I believe your setup is straight forward. You may want to wait for the more knowledgeable to verify or elucidate before acting on what I am about to relate.
You have two wet-cell 12v batteries physically wired together, not through a switch or combiner circuit. With this configuration, you essentially have one 12v battery with twice the amperage capability of a single battery. As such, you should set the charger for one battery. Since you are experiencing difficulties, I would clean all of the terminals and check the electrolyte levels in the individual cells (if you have not already done so). With the batteries separated, you can charge them individually if you choose. My preferred charging arrangement would be with them interconnected, and with the positive charger cable connected to one battery and the negative charger cable connected to the other other battery. If this configuration does not work, disconnect the batteries from on another and try charging individually; you could find that one of the batteries has a problem.
Having reread your posts, it appears that your problem was in setting the charger to "Both". I'm guessing (always a bad idea) that your charger has two sets of cables. If so, you should be able to disconnect the batteries from one another, and charge them individually and simultaneously using the "Both" setting. This discussion may be pedantic, but it could help you to understand your charger.
Last edited by jones2r; 11-28-2006 at 12:16 PM.