I'm told, but have no experience with it, that a boat bouncing around in rough water can damage a battery.
With my charger no matter how charged the battery is every time you disconnect the charger from house current it will tell you it is charging the battery from below the 80 percent state. You would expect the opposite problem because of what they call surface charge where a bad battery will give you higher voltage immediately after disconnecting it from the charger than it can actually maintain. Checking the charge of a battery by voltage is not very accurate because it is a chemical process. I'm fairly suspicious of all of the new fancy chargers. There are so many things to consider such as the ambient air temperature the temperature of the battery itself, how recently it was used, and a bunch of other consideration that a truly automatic process that would maximize battery life would be difficult to achieve. I understand that there are newer battery chargers that take into account ambient air temperature and allow the user to customize the charging regimen. It all sounds like a lot of bother to me. When I was young and poor I float tested my batteries regularly and manually controlled the charging regimen. Now I just replace them.
One thing I think you should do if the battery charger is giving you weird behavior is put a load on the batteries and then recharge them. That way the various problems with measuring charge by voltage is going to be more less of a problem because you will know you are actually charging a drained battery.