Thinking about that trolling motor, maybe it is the culprit, but why only one battery draining?
So, you said you charge both batteries separately and the trolling motor is always connected. So when you charge them, you must be disconnecting the wires in order to separately charge them. A dumb question, and trying not to insult you, but at any time is the trolling motor still connected to one battery while the other is charging? Probably not since it seems obvious...but I figured I'd throw it out there....
I would take that trolling motor out of the equation, charge both batteries and see what happens.
So, you said you charge both batteries separately and the trolling motor is always connected. So when you charge them, you must be disconnecting the wires in order to separately charge them. A dumb question, and trying not to insult you, but at any time is the trolling motor still connected to one battery while the other is charging? Probably not since it seems obvious...but I figured I'd throw it out there....
I would take that trolling motor out of the equation, charge both batteries and see what happens.