Hi BFL13,
It has to do with small differences in resistance that end up causing much larger imbalances. The terrible thing is that jars on the "ends" of chains never ever get fully charged. And you, of all folks, know exactly where lack of 100% charging leads.
Since, in effect, you have 3 twelve volt batteries, the only way to balance them is method #3 on the smart gauge site. But the three are not equally sized so I suppose one could mess about with extra connections and/or longer wire to try to use increased resistance to over come that issue.
I believe you take better care of your batteries than almost anyone else here, and certainly more care than I do.
