re: On board battery charger and new batteries not charging.

Even if that charger was giving them the full rated output those could take longer than a day to charge if they were low from sitting on the shelf. Deep cycle batteries would still spin your motor well while still well away from a full charge. You'd need some extra tools to see what the current and voltage the charger was putting to each bank, it's probably not using all 5A due to the condition of the batteries.