HCL,
As A.S. states, it would be helpful to have the NI Spy Capture of the actual commands that are being sent in your case. Also, what do you mean by the "UUT is rebooted"? Does this mean after one unit is done testing, or is there an actual code module that reboots your UUT?
If this is a driver related problem, then you should be able to reproduce this in any programming language. Have you seen similar behavior in LabVIEW without using TestStand? Does it only happen with your sequences?
Thanks,
Shannon R.
Applications Engineer
National Instruments