I recently had the same thing going on with mine on the cranking side. The battery was only at 1% and needed replaced. Once I replaced it the charger started working properly and charged my batteries....
It's all coming together and we have you covered @ Shut-Up-And-Fish LLC
for all your Humminbird, Minn Kota & Motorguide needs.
We do Installs!!! 972 737 8161