Battery charger is a 2 bank charger. Only 1 bank is coming on and chargeing. Disconnected and put manual charger on and battery was charged. Any suggestions or ideas. Please

With respect to "being charged": If it was your starting battery, it's possible that the outboard had sufficiently charged the battery to explain how the battery was already charged.
What makes you say only one bank is charging? LEDs not coming on, or have you measured the voltage on the battery with a voltmeter while charging?

Swap the bank 1 and bank 2 charging leads and see what the charger does. It's best to have a voltmeter to check each battery before charging, and while charging.

Thanks for comments. Swapped out as side and 1 bank dead. Installed new minkota. This was to trolling motor batteries