It's not the number of type of batteries. The Intelletec enters Gen mode if it senses +12v on a wire that is active when the genset is running. Usually that is wired to the remote start switch light, but different RVs can and do use different sources. My guess is that somehow when rewiring the batteries you shorted something to the circuit that the Intelletec uses to detect Genset running. Is the generator remote start button also lit up? That would be a clue!
In any case, go back and check your battery wiring. Probably one of the small wires, not the big red ones. Something left off, or wrong terminal, or shorted...
Former owner of 2004 American Tradition and several other RVs
Home is in the Ocala Nat'l Forest near Ocala, FL
Summers in Black Mountain, NC