The one series battery is basically doing twice as much work as the two paralleled ones, hence it gets abused when they loaf along. Twice the current is flowing through it as each of the other two, and thus it's supplying or receiving twice the charge as the others.
Frankly, I don't think three 6V batteries connected in this way is a good idea at all, and not giving you any real benefit over a simple pair of 6V batteries in series. Your total usable battery capacity is limited by the single battery, and there's a tremendous imbalance between it and the other two. A better plan (if two 6V batteries are not sufficient for your needs), and one that would have a larger usable capacity than what you have now, would be to have a pair of 6V batteries in series, to form a single 12V battery, and put that whole assembly in parallel with a 12V battery. If there's room, four 6V batteries (wired as two 12V batteries in parallel) would be even better.
