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Thanks for your post.
I would have thought that the connection timeout would be the same through the command line as it is through the GUI, but you may want to try manually adding a timeout value to the command.
You can do this by adding the connection timeout parameter. e.g.
/server1:"<server>\<instance>;Connection timeout = 300"
If this doesn't help. Can you post the error message?
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We have one profile that keeps timing out when using the command line utility (via a scheduler) but does't when using the Data Compare GUI.
I don't think it's the scheduler that's timing out since the data compare is actually writing that fact that it's timing out to the log file.
Anyone have any thoughts?