Wiring an inverter, especially an add-on to an existing electrical system, can be confusing. It sounds to me like you have the inverter's AC output connected to a circuit that also is powered from your generator (and maybe even shore power). This is a big no no. See this diagram - Xantrex Diagram
Any outlets that you want to power with the inverter and generator/shore power must
be wired directly to the inverter's AC output and not directly to any other power source. The inverter will sense when generator or shore power is provided to its input and will switch off the battery feed automatically. If you're having to flip a breaker to avoid damage to your inverter, then you need to rewire.