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Current dev sources, Metal L&F. Make sure the O.W. has one tab in it. Maximize the window. Discard the output. A gray box is left on screen where the popup menu to discard the output was shown; and if you switch away from and back to the IDE, the whole main window between the bottom of the toolbars and the top of the status bar is blank grey. If you unmaximize (e.g. S-ESC) then everything is fine again.
Yes, I experience it too. Just there has to be two tabs when maximized. The problem is the output component is remnoved from the GUI hierarchy(!) when removing its inside tab (when there is only one inside component it is not shown in tab).. I will investigate it.
Fixed in [trunk] core/windows/../view/SplitView.java 1.3
verified in NB 3.6 RC1