I do not have enough details to answer this properly, however, you may have a problem due to the type of load you have on this machine. Electronic controls for generator sets today us zero crossing to determine the appropriate frequency. If you have three phase or single phase rectifiers as the major load, voltage notching caused by semiconductor commutation could cause the frequency variation which in turn affects the load impedance thus changing the output voltage. Look for this type of loading characteristic and add filtering as needed to the voltage sensing circuit of your generator.
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