I think you need to find a dealer who is more forthcoming!!! A magic box, come now!!! But your discription sounds like you have a parasite voltage problem drawing down you house batteries when not hooked to shore power. You still have things in your coach that use power, like the smoke detector, LP leak detector, Carbon Monoxide Detector which are all operating. These items draw down your batteries.
And "Thinking the charger was not working I checked the voltage at the batteries while plugged in, 13.9v. I unplugged and checked voltage on the batteries, 12.7v." That sure sounds like it is working to me. 12 volt deep cycle lead acid batteries should measure 12.6 to 12.8 volts when fully charged with charger not operating! How long it can hold that 12.7 vdc is the question!!