Have you tried other settings for C1?
Have you configured "Built-In Input" PLC settings correctly for your Sensor Input. Should be "Use Counter [60Hz]", "Linear Mode", Software Reset", "Increment pusle input" [Don't forget to power down and power up PLC after changing them]?
What IS the RPM range of the shaft?
Other things to consider:-
Switching frequency of proximity switch. Are you operating the proximity switch outside its switching frequency [a very common mistake]?
If the RPM is slow and/or the duty cycle of the pulses is not consistent [all 6 pulses should be about the same] then you WILL se fluctuation.
In that case you will need to create an average speed over a longer sampling time to smooth out the result.