There is a chance that if lighting comes in the power source, it will burn up everything. That is why they tell you to unplug your trolling motor. As far as ATM's batteries not charging up to 100% capacity, I would : 1. Make sure all leads are connected correctly. 2. Go buy 3 new batteries. Go to see Torch and get a deal.
The old Ranger boats asked that you unplug your TM.