OK, now we're getting somewhere.
First, I agree that it's very likely your Lifeline batteries are AGMs, not gelled cell batteries.
I also agree that the grouping is rather strange, and it would be beneficial at some point to connect the two 4Ds together and run them as a single 420AH house battery bank, and to use the 100AH battery for starting.
You didn't mention a battery combiner or echo charge device. How is the alternator connected?
Since you already have a 1-2-Both-Off switch, an easy way to improve the setup would be:
1. Wire both 4Ds together in parallel, and connect this bank to position #1 on the battery switch.
2. Wire the 100AH battery to it's own ON-OFF switch and to the start solenoid.
3. Run a cable from the the new ON-OFF switch to position #2 on the battery switch.
4. Install an EchoCharge or DuoCharge device, connected between the house bank and the start battery. This device is completely automatic, and bleeds some of the charge off the house batteries to keep the start battery charged.
5. Connect the output of the Balmar 110A alternator -- and all other onboard charging sources (battery charger, generator, wind, solar, etc.) to the house battery bank.
6. Leave the switch in the #1 position. The "BOTH" position would be only for those very rare times when the start battery is depleted and you want to start from the house batteries.
Now, about the original question re: charging amperage.
There may or may not be something amiss. AGMs can absorb A LOT of amperage...all your 110A alternator can throw at them...and more. The MC612 controls how much amperage is going to the batteries, based on its internal charging algorithm ("program") and upon external factors such as battery voltage, battery temperature, and alternator temperature (assuming these sensors are fitted).
It's really a quite sophisticated system, and works beautifully once set up correctly. There are some potential bug-a-boos, though.
In order for things to work correctly, you need:
1. the correct program chosen in the MC-612 (i.e., PO4 AGL);
2. all sensors correctly connected and working properly;
3. adequate size wiring;
4. clean, tight connections; and
5. alternator belt tensioned properly and not slipping.
The best way to easily check re: output is probably to take the boat out, drain the house batteries to about 50% charged state (about 12.3VDC with NO LOAD and NO CHARGE after sitting for several hours...as measured with a reliable multimeter AT THE BATTERY TERMINALS).
Then, when you start the engine, after 40 seconds or so you should see the amperage ramp up to somewhere over 80. If you see this, then the system would seem to be basically OK. However, if you only see 10A or so, something is definitely wrong.
Note that temperature sensors can give improper readings. If you suspect a bad temp sensor, just pull it's connector off the MC-612 and see what happens.
Finally, don't worry about the readings you get from the battery monitor -- at least not until you know it's been properly calibrated and you've lived with it awhile. These things can be good, but they can also give very misleading information.
Sorry to be so long-winded. Hope this helps a bit.
Last edited by btrayfors; 08-25-2009 at 02:45 PM.