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The new installer (used in M9) is using Swing PLAF decorated JFrame on Linux, which touches this JRE bug: http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5079688 I would recommend to not use this feature, at least not for non-fixed JREs (none available yet).
I've added a system property which will control this behavior. By default the window decorations are expected to be done by the system window manager.
*** Issue 109689 has been marked as a duplicate of this issue. ***