It sounds to me like your charger half of the converter/charger box isn't working.
I also think that possibly your house battery setup could be the issue. You are wiring two different setups toegther - the 2-6v batteries and the 1-12v battery. That could possibly(?) have messed up the charger.
I would try disconnecting the 6v batteries from the 12v battery and charging them separately with a portable charger. If they charge, then it's your charger or the 2 types wired together. In that case, wire only the 2-6v or the 1-12v to the converter/charger and see if it charges from the generator.
