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I'm not a fan of remote debugging
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Tell me about it.
Perhaps it would help to verify in Begin whether they are using the Auto Independent or Auto Iterative. I'd suggest the independent.
Open the VI and reproduce the issue. You can put down probes, turn on exec hilighting, or pause from time to time to see where the code is. Is there a loop that doesn't feed or delay & feed?
If you get it down to that VI, post it and I suspect someone will spot the issue.
Finally, I did run into teams who simply press the Run button on auto and were surprised it didn't work. Make sure they are running auto by running main and putting the DS into auto mode.
Greg McKaskle