A couple odd scenarios come to mind...
Based on the idea that the owner was switching banks, he might have an unusual setup in that only one bank is charged at a time? You never know what kind of custom work people do, intelligent or otherwise.
Also, maybe the boat was sitting with the charger
off for a long period of time and flat batteries. Possibly, he thought turning it on a few minutes before your arrival would be sufficient to show the boat. Did you turn on a lot of DC items when the alarm went off?
Either way, something is not as is should be. Delve deeper if this boat is one you are interested in.