Re: Battery Charger and Battery Switch
Lobo, I'd suggest "divide and conquer".
Break up the system and examine each piece to see which one is bad. Fix the bad ite, then come back to look at the system for system faults.
So first, pull the battery cables and test the voltage on each battery using a known good voltmeter. Ah, "known good". Yes, it is possible that your handheld iff off, or the panel meter is off. I've seen panel meters off by more than two volts, handheld digitals often off by 1/2 volt on a 12-20 volt scale. I got so tired of this nonsense that I went out and built a meter calibration reference gizmo, it puts out 10 volts within better than 1/100th of a volt and if the meter doesn't agree--I know the meter is wrong. In your case the simplest thing might be to go to WalMart or Target and spend $25 on a new meter, two out of the three will probably come close to agreeing.
Also, if you are testing voltage while any charger/alternator is running, you may be seeing an error if there is AC leakage or some type of pulsed DC on the line. Take your readings with JUST battery power connected, see if there's a difference.
If the batteries are OK, they'll range from 12.6 (perfect) to 11.6 (useless) depending on condition and state of charge, after they've been allowed to sit unused overnight, or after a short load (turn on everything for two minutes, then turn it off and rest for five more) has been applied. That's not perfect but it is good enough for now.
If the batteries are OK then you need to check the charger, which can be harder. You'd need to check the output for proper voltage under load, and for any AC leaking through. Often the best way to check out a charger is to first check your battteries, then if the batteries are OK, see if the charger is working. Swap it out with a cheap battery charger, even an auto battery charger, and see if that works when the boat's charger doesn't. If the other charger works, time to send the suspected one out for testing and repair.
And of course sometimes you get lucky. If you take a pencil and sketch out the wiring of the system, and clean and tighten all the connections, sometimes that's all it tkaes to find one loose, dirty, or wrong connection that fixes everything. If you're lucky.
But you still might want to "divide and conquer". Start with the batteries, you can also take them into any battery store and have them tested if you want to make the job easy. (Except for the heavy lifting of course.)