Were the circuits tripping while running on generator, or while on utility power, or both?
Is this a 3-pole or 4-pole ATS? If a 3-pole, did you disconnect the grounding jumper in the generator? If a 4-pole, did you double-check to make sure the grounding jumper is there? I wouldn't expect a double-bonded neutral to trip any circuit breakers, though, it's more of a safety issue. A floating neutral can certainly cause issues.
