I would think, if you have a 'short' on the house battery side, you would see it popping breakers on the DC circuits. To answer your question about the alternator and the inverter/charger, the DC from the alternator to the house batteries doesn't go thru the inverter at all. That only comes into play when on shore or generator power. The inverter/charger takes 120VAC and turns(converts) into 12VDC to charge the batteries. Unfortunately, it sounds like you are at the mercy of the guy doing the install at this point.
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