What is the ratio of the slots to solid ? If you can keep the sensor from seeing a transition during the settling time it should eliminate the problem for now. This is in my opinion a kludge not a proper fix.
The mass of the load that will be added (if any) to the rotating mass when the motor is in the machine may affect this situation. Any external vibrations that will be added to the mix when the motor/encoder is installed will also affect the actual operation. Terry