Is it possible that you've never really charged the AGM for the windlass fully enough? As such, might have walked down the capacity of the battery by sulfating it. Most Optima start batteries get "over-charged" which doesn't really hurt them much. in my opinion, you should be seeing 14.5 volts going to that battery for a bunch of time whenever you run the engine. You might test its real capacity. We had a set of AGM's which were replaced on warranty. They'd start-out at decent voltage, but would quickly show that they had no current carrying capacity.

Gooffy things happen with the load going "out" one side of joined group; and, the rest of the bank "topped" out, etc.

Having a Combiner (like those sold by Andina), might help. But still you need to deal with which bank gets the "most" charge.

Anyway, Neil might invest in the regulator which allows for two banks to be independently smart-charged charged from his smaller alternator.

By the way, I had to boost the charge levels to match what the batteries were actually "seeing"