Wow! Thanks for all of the replies folks!
To clarify, I have checked the battery with a mutimeter by taking the red probe and putting it on the + side of the battery, and the black probe to the - side. BOTH batteries, engine off, battery charger not plugged in - indicate 12.6v. Although multimetering the posts of the battery return good volts, my dash gauge shows lower volts on the #2 battery, with engine OFF. With engine on, for some reason #2 will also get overcharged (16v+ at times!).
Using the multimeter on the battery posts, when running on #1, it will show charging around 14.5v or so. When Im running #2 battery, it will show charing at 15-16v+.
Both batteries share a common ground. My #2 battery black battery cable goes to the back of the engine block. #1 battery is connected to the #2 battery via a cable thats about 2' long and just goes from the - post of the #1 battery to the - post of the #2 battery. My last Four Winns (99 Vista 258) was set up the same exact way.
I bought the boat April 2010. Ive noticed that there are several parts of the red battery cables of both batteries that have black electrical tape wrapped around them - Ive taken the tape off and there is no damage underneath. I have no idea who wrapped rings of electrical tape around the positive cables and why

After all, the boat is 20 years old and Im the third owner.
How could I rule out a bad battery cable? It seems on the #1 battery, the boat is getting the full power out of the battery but on #2 some of the volts are getting "lost" somehow along the way. Maybe the alternator doesnt sense that #2 battery is charged fully, thinks its discharged because of loss of volts through a bad cable, and overcharges to compensate??? My head hurts...lol.