Welcome to the forum. I don't know your 2006 specifics but I think you have the RV Custom BCC in the engine bay driver side. Inside the BCC there is a grey colored 50 amp cct breaker with a small black reset button on it. Check to make sure that button is pushed in. If it has tripped the open breaker will prevent the converter (battery charger) from connecting to the coach battery or the chassis battery for charging. Take care opening and working inside the BCC. Grey breaker shown in lower left corner of attached jpeg.
What concerns me though is you say with shore and gen off and coach battery disconnect "on" you get lights working normally. If the BCC 50 amp breaker is tripped, you should not get any coach battery connected to the coach 12vdc fuse panel fed from the converter. Maybe I missed something in your description though.
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