+1 to what smac said....
was that 12.0 volts under any kind of load, or at no load, or at no load and rested at no load for some time?
if the measured voltage was under load, then yes, your batteries are somewhere "about" 50% state of charge...... which for flooded cell batteries is as low as you should discharge them with any regularity, and they should never be left in that state... so good on you for trying to charge them....
if the voltage was at no load (or very low load) , or worse, no load and rested for some time, then your batteries are "about" 100% discharged, and should never have been drawn down this far (except in emergency
pumps spring to mind).... in this state, the lead suplhate created by discharging begins to change form greatly increasing the batteries resistance to charging.... bear in mind that to limit your charging current
to 35A, a TOTAL system resistance is 0.068ohms - that is why everyone is telling you to check connections, one dodgy connection could easily increase the resistance by that much, or more.... if it is over discharged, that might explain the initial resistance to charge, and you might have just caught it in time to save the battery from permanent damage.
to elaborate a little more on what smac said - in your car, the alt will not put out its reted amps until the engine is spinning at 3000 rpm
or more (at which point the alt is doing ~8K rpm...).... on your boat
, the pullies will be different ratios, but the idea is the same, at idle, the alt may not charge at all, it will need to be well above idle speed to do any meaningful charging.
then there are the vagaries of how batteries charge, and how charge current tends to taper off over time - to get 200Amp hours back into your 400AH bank, will probably take 6-8 hours of engine time at speeds well above idle - and this is without consideration to any load you may have (fridge, lights, radios etc...)