What the OP did is thinking so far out of the box it isn't even on the same planet. I googled connecting 3-6's in a 12 volt configuration and no where was there an answer. I know what he did, but why? It is no surprise he is cooking one battery. There is no way one could get balanced charging or consumption out of such a configuration. I'm guessing he only has room for 3 batteries. If so his best solution is 3-12's. Next best solution, but not ideal, is 2-6's and one 12.
In short, the answer is unbalanced charging. There is no way to answer this without giving an opinion on his battery configuration as is is the cause of the problem.
