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6.0, jdk1.6.0u3, linux, gf-v2.1-b11 -start server from the IDE -exit from the IDE => dialog showing progress on stopping the server should appear, but only empty dialog which does/says nothing appears - see attachment
Created attachment 53987 [details] screenshot
Is it reproducible for you? Are you sure this dialog is consequence of closing netbeans? GF usually doesn't show such dialog afaik.
Can't reproduce in any way.