Find your charger model number and post it. You may be better off replacing the charger with a modern three stage unit. I had a MH that only charged at 3 amps. That was an 89 model and yours is later but it is worth looking at.
I tried to find the converter/charger model for your unit and only came up with MagnaTek 6332 . This may not be it but is a good indication to me that your charger may be very wimpy.
These chargers share their outputs. For example if your charger puts out 40 amps and your heater is running and you have lights on you may be charging the batteries at a very low rate. Getting a better charger will supply plenty of power for the systems and battery charging,.