My guess is, one of your banks is faulty - your cranking battery is charged by the outboard so you never noticed that the charger wasn't charging it.
To test that theory, swap the batteries and banks and try again. First disconnect the trolling motor leads from the batteries, to rule out any possibility of wiring faults.
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"The metric system never really caught on in the states. Unless you count the increasing popularity of the nine millimeter bullet." -- d. barry