frequency measurement keep reading value when stop rotation

Hi,
i am doing the program in the attachment 
in this program i am using ni9401 and cDAQ 9188 to measure frequency from motor driver 
but i am facing some problems 
1. the reading sometimes different than osciliscpe.
2. when i stop the motor the program still read values and not going to zero |
Note my driver send the feed back as a signal"Pulses" with difference frequencies depend on my speed . i send digital values to the driver pins 111 to make it rotrate forward and 100 to make it stop rotating + analog value to change the speed 
can i have help in that ?
thanks