They should be pretty quiet and smooth. It is normal to have a knocking sound on a used machine during heavy or interrupted cuts. The knocking comes from the drive spline.
Is there anything else you can think of to describe this noise and exactly when it occurs? You mentioned it's quiet in neutral - how are you selecting neutral? Is the noise relative to spindle speed or is it constant? Is it quieter at higher RPM? Do you have the downfeed engaged?