Hello,
What type of operation are you seeing reset?
If you are using DAQmx in C#, then you should see something like pulse train generation end when the program exits. The reason is that the DAQmx driver ends the pulse train. You can find more information on the DAQmx driver
here.
If having a pulse train continue after a program has terminated is a desired effect, then you could use our Traditional NI-DAQ drivers in order to accomplish this.
Justin T.
National Instruments