Here is a snippet of code in c#/.net

string stdout = server.Jobs.Tasks.GetOutputString(OutputInfoClass.OutputT.StandardOutput, JobID, task.Id, true);
string stderr = server.Jobs.Tasks.GetOutputString(OutputInfoClass.OutputT.StandardError, JobID, task.Id, true);

stdout will fill incorrectly, but stderr will be an empty string.

If I run the second line again it will populate stderr correctly. Is there some kind of flush I am missing?

Not that we are aware of. Which version do you use now?

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We are using version 1.0.1.19710 of the api dll, and version 7.5.1 of the server/client.