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Ubuntu Linux, JDK 6.0u2, custom theme (Simple controls, Metabox window borders) The main menu bars which have icons next to some of their items, like e.g. File menu has, have an unnecessary extra empty space at their left side. I was not able to take screenshot with a menu bar open, but you can see this easily if you compare for example File menu with the Navigate menu. I don't see any icons in the Navigate menu and the extra empty space at the left is not there.
To be fixed soon, TM = 6.0beta1.
Unfortunately, this is JDK GTK L&F bug. Every time menu has a submenu, extra space will appear. Entered as jdk bug 6575091, with all info and test case. http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6575091