Why does some part of acquired signals repeat at the beginning and ending of signal?

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I'm acquiring some pulses which repeat at certain intervals. Hardware is Advantech pci1710 (it is like NI multifunctional pci cards), software used is Labview 2013.

The problem is: at the beginning and ending of pulses I see some added pulses which I'm not sending to the device! What are these pulses and their origin and how to fix it?

Pulses screenshot >

Messy signals

Red signal and white signal are both about 500 HZ Square wave which repeat one after each other (number of pulses sent to each channel is limited. They are in fact pulses generated using Arduino to control a servo motor driver).

program written in labview

sampling pulses vi has two signals sampled and are default values on the graph. readback vi has one signal sampled and is the default value on the graph.

on the read back vi I have written a code to count the number of pulses .

what I found is that: I'm sending 2000 pulses but each pulse is divided into 3 parts , the first part and the third part vary and the middle pulse is almost fixed . if I sum the divided parts it is 2007 pulses and near to the 2000 pulses I send .

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