Brian,
George is right on the money on this one. I think he pinpointed the problem but if not I have one more thing to try. Your noise gate may be set too high.
The noise gate mutes the input from the microphone. If its set too high, it can lower the volume of your mic setting enough to prevent triggering the harmonizer. If you sing softly, this could be the problem. Refer to page 82 of your 9000PRO manual to ajust the noise gate. Luckily, Yamaha provides us the ability to reduce our noise gate to zero (if we want), so even the softest singer can be accommodated.
Regards,
Steve
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