Found this on a Seaswirl forum. Sounds like it is factory wired that way. Bat 2 shares the ground with bat 1. Unless it is hooked up to bat 1. it isn't grounded. Should be an easy fix ground bat 2.
I know that on my 2101 striper, from the factory, with the perko switch, wired the way the factory wired it, I will not be able to start my motor using battery #2, with the perko switch on position #2, unless there is a battery / positive and negative cables are connected on battery #1. This is because of the way the grounding is done (battery can be dead, but the ground is what is shared). However, I can start the boat using battery #1, using switch position #1 if nothing is connected to the second battery.