We'll need more information to help you.
Type of generator? How does it connect to the power system on the boat?
On my Cutwater there is a rotary switch to feed gen output to the system. You can switch from shore, to inverter, and to generator sources of electricity. With the genny on do you see power on the dial on the power panel?
There is usually a circuit breaker switch on the genny itself. So it's possible that the motor will run but not output electricity to the boat. With the genny on do you power to other items on the boat?
If you have the combination inverter/charger setup there could be an issue there too.
-martin610