I have a 2 bank onboard chargerm for the trolling motor and one of the positive charging leads gets really hot. I cleaned the posts and the connection seems good it doesnt seem to help. What would be the cause of this? It smells hot after being on for a while and i dont want it to melt or start on fire. 
I would have the charger checked for the proper output on both banks, sounds like something could be wrong on one bank inside the charger 
A couple of things for you to check would be: 1.Check the entire length of the wire for any breaks, rub through’s where it could possibly ground to the boat 2.Load test the battery to double check that it does not have a bad cell. Do as above post said too. 
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