Still need to know if your 120v from the various receptacles is ok for voltage and three-light with generator supply, so you don't fry your microwave etc.
Which model Boondocker? The older model 100 amper has a shaky thermistor for the 120v input that can make lots of smoke (don't ask :) ) it also has a 125v glass fuse at the 120v input that could smoke. You have to do something special to get the thermistor to smoke. The newer ones have a beefier thermistor (lesson learned!)
If all the other 120v things were ok on generator, not just the breakers with nothing on, but with 120v appliances on too--- then we can zero in on the converter issue, but if the 120v is bad from gen but ok from inverter and shore power, then we can return to the generator or transfer switch, etc.
Do you know for sure you were on the new converter for that 12v stuff on shore power, and not just on batteries? (13.x v instead of 12.x v) So the batteries are ok and not the reason the converter fried?
Got to zero in on what to be looking at. ( I am still thinking about that earlier surge incident)