Unexpected Data

I have two controllers cRIO 9068 (OS is NI Linux Real-Time) and cRIO 9081 (OS is Phar Lap ETS). They both have the same analog input card NI-9229. They are both viewing the same analog input (Neutral Current Low in the VI file). See attached "Wiring" sketch for details. The attached VI snap shot is shown "VI snap shot". It is set to sample 1000 times per second. The signal (i5th) is 300 hZ. The FFT sample is set to 200. The issues i am seeing are the following:

First, i would think that 1000 samples per second and an FFT sample of 200 the maximum amount of decision it could make it one second would only be 5 (1000/200). However i see the following:

A lot more than 5 decisions in one second.

Second, Even though both controllers are looking at the same point the cRIO 9068 sees all events almost twice as much as the other controller (cRIO 9081). They both have the same VI files complied to them. Why is this happening? How can i troubleshoot why this is happening? 

Third, What can I do to filter out this "noise" (if it is that). Looking at the high setpoint and low setpoint (not shown in the VI snap shot). it shows it going to the upper limit, back to normal, than to the lower limit in one second many times. There is no way i believe this analog input is really doing this. Especially since both cRIO do not see the same data.

Any input would be appreciated.