I don't understand, 3 batteries on one bank and one on another and,,, then combining them while you're using the boat. Starting the engine on the one battery and then throwing it into the bank when you shut the engine off. I can't think of any advantage to have or use a system that way. You've got a lot of stuff going on. Perhaps it would be in your interest to reconfigure your battery banks making a simpler straightforward system for better battery management. The Link likes it simple. We have one big house bank and one separate engine start battery. The only time they may get connected is if the engine battery is bad and I push the 'parallel' button at the helm to emergency start the engine.

I guess I'm saying that I have no idea what the problem might be but think that making it simpler might be a good start. Shouldn't take long at all.