I don't see how an "Intellegent switch" would solve it, as the problem is there when running on one battery.
I assume the same fault occurs when switched to either battery.
Connect one of the batteries direct, bypassing the Battery switch, I suspect it's a fault in the switch.
I've had the same set up as you on my previous boats and never had any charging problems, I used to start on Bat1 run for awhile to put back what was drawn by starting and then switch to Both. When I stopped to fish, I'd switch to Bat2. Next trip out I'd start on Bat2, run on both and switch to Bat1 when stopped. This way both batteries got the same treatment.