Steve,Joel,
I misinterpreted your battery wiring question, got my series and parallels out of whack :-)
As far as the answer to your question, we basically all have our banks wired with 3 pairs of six volt batteries wired in series to make 12 V and then the three pairs are wired in parallel by the factory wiring harnesses for increased current capacity as you know. There is little difference between paralleling two larger banks of 6V batteries and then putting those banks in series or the three series pairs like we have now.
There is a difference in discharge rate of individual batteries within the bank based on how well balanced the wire resistance is and where the load connection points are made. Steve, I do not think the wiring configuration explains your battery bank performance issue which is either more current is being drawn then you think, or the battery capacity is not as needed, or the attained charge level is not right.
You can read the linked article and visualize your connection method and see if you have some balanced lengths of wire from the banks to the load. This wiring variation is more of a subtle capacity loss issue that would not explain your problem in my opinion.
I think the best way to go about sorting this out is to put a constant load on, maybe 25 - 40 amp range, and then with the use of a clamp DC amp probe you should be able to see what current is coming out of the bank and how balanced each battery is contributing to the load. With the charger off you can plot DC voltage (bank capacity or charge level) vs time at constant current and see what the bank will deliver in amp hours. You can also measure DC volts of individual batteries and see if they are discharging at the same rate. You probably will have to lift a terminal wire momentarily to measure that at intervals. Hope you can find the issue.
http://www.smartgauge.co.uk/batt_con.htmlLater Ed