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[HenryGR <henrygr@xxxxxxxxxxx>]

Not fully sure that the problem is Java, I got the same issue using Firefox, Bluefish, ....
Anyhow, I am using:
Ubuntu 11.10
Gnome Shell 3.2
OpenJDK java 7 
   Version: openjdk-7-jre 7~b147-2.0-0ubuntu0.11.10.1

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which is subscribed to openjdk-6 in Ubuntu.
https://bugs.launchpad.net/bugs/777425

Title:
  Menus unusable with gnome3 when windows maximised

Status in “openjdk-6” package in Ubuntu:
  Confirmed

Bug description:
  When using java applications on natty such as netbeans or arduino and
  openjdk in combination with gnome3/gnome-shell from the official ppa
  if a window is maximized the main menus are unusable.

  - when you click on a menu, it disappears as soon as you release the
  mouse button.

  - when holding the mouse button and drawing along the menu (from File to
  Edit for instance), nothing happens (the File menu remains opened the
  Edit menu is not visible).

  - when dragging further on the right, the Edit menu is finally
  displayed, but the mouse is on the Refactor menu

  - It is almost impossible to select an item in the menu and when it
  finally works, you cannot select a sub-menu item

  This problem is not resolved consistently by using sun-jre.

  I am using the latest openjdk package 6b22-1.10.1-0ubuntu1 in a clean
  install of 11.04

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