1) Yes, this is probably why. A 3400 watt generator should be plenty, but if you have a large battery bank AND a converter sized to properly charge it, it is possible to overload even a 3400 watt generator. This is why the rigs with built in generators often have 4,000 watt and up generators.
It is easy to draw too much power. It adds up. The converter uses a little just to run, much more if it's trying to charge the batteries, a few lights, refer control board, ditto the water heater control board. A few watts here, a few watts there, and pretty soon we're talking about a real draw. (With apologies to Mike Mansfield.) And then you fire up the AC.
The usual RV battery condition idiot lights are mostly worthless. If you start a trip with the batteries at full charge, there will be enough current from the TV to run tail lights, turn signals, and maybe the refer control board, so maybe you will arrive with batteries still full. Shut the truck off, however, and they start discharging. But it will be some time before the idiot light will report anything other than full. Fire up the generator, and the converter jumps in, sees less than full voltage, and slaps full bulk-charge power to the batteries. Two hours later, when the converter is scheduled to cut charge down to maintenance level, THEN you would be free of that load. Mostly. But you are right, you probably should leave the battery cutoff ON when running the generator.
2) not exactly. The Refer does use a small amount of 12 volt power for the control board. Ditto the water heater. Not much, but a little.
3) Not sure what this looks like.
4) Being at more than 5,000 feet no doubt played a part.
A Hard Start Capacitor would probably help. Worth a try.
Good luck figuring this out before the next boon docking adventure.
