Multifunction DAQ

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can anybody suggest possible way out: why restart after ntp sync ?

 I am setting computer time fron NTP service every 15 minutes, my labview program reads computer time and for every second it generates a pulse on one line of a port of DAQ6216. this works well till computer do not call ntp server and resynch. my program even if running do not record change in second and hence do not generate any pulse. i have to restart the system ? why is so ? can anybody suggest posssible reasons and their remedies..plzzz also i m not able to measure round trip delay of the system check attached file

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