Have you tried working with a Tableau Packaged Workbook?
This may change it's behavior.
I haven't, but I have used query extracts many time before from the same database without a packaged workbook. I will try saving it as a packaged workbook now.
I seem to get the same problem with a packaged workbook. Though if I reduce the time period that the query looks at (i.e. reducing the amount of data query looks at and the length of time the query takes) the the extract is created.
I am fairly sure I have successfully more intense queries before though, so I'm not sure what is going on.