make sure that there is a bit of mechanical vibration introduced into the encoder so that the shaft of the encoder experiences ISV with respect to body of the encoder. (ISV == Instantaneous Speed Variation). Under these conditions you will surely see the issue.
Michael, I have yet to see a mechanical coupling that required you to "make sure that there is a bit of mechanical vibration". I know of no gear or other coupling that will not show this. The obvious difference will be to what extent the problem will show and I have found that the tighter the coupling the higher the frequency of the 'noise'.

Erik