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When you close a HTML application (with "X") while it is a running as AUT, it is still present in the Running AUTs View, you can even start a test execution ("Now testing" till a timeout, because now AUT is there). When you close another AUT (with "x"), like SimpleAdder (swing/swt) or DVDTool it disappears in the Running AUTs View.
This is not yet an eclipse related issue.
Closed not Eclipse