The generator is not connected through the battery isolation/disconnect contactors because the generator's starter motor requires a large current when cranking (in the rough vicinity of 100A average, presumably with peaks well above that, on the generator in my motorhome).
This sounds like a generator problem or generator control problem--an auto-generator-start controller if you have one, say--as much as anything. It might be something as simple as one of the generator control switches sticking it the "off" position rather than properly in the neutral position. It may be that the generator just thinks its in a fault condition rather than actually off, and merely interrupting its power would reset its little brain.
