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The issue in my post appears to have been resolved.

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https://bugs.launchpad.net/bugs/1110138

Title:
  Unity: wrong window dimensions / location in Java applications

Status in Compiz:
  Fix Committed
Status in Java OpenStreetMap editor:
  Unknown
Status in “compiz” package in Ubuntu:
  Fix Released
Status in “openjdk-7” package in Ubuntu:
  Confirmed

Bug description:
  In Java applications, the functions to set and get window dimensions
  and position do not work as expected. This problem is only observed in
  Unity but not gnome, Win., etc.

  Details:

  * Call setSize(200, 200) and setLocation(300,400) for a JDialog
  object.

  * If you call getSize() and getLocation() directly after making the
  JDialog visible, the result will be (200,200) and (300,400). Calling
  getSize() and getLocation() again, a split second later, the result is
  now (200,200) and (301,428). In both cases, the values are wrong, the
  size and location is actually (202,229) and (300,400) as shown by a
  screen capture.

  Consequences:

  * If the dialog is designed to reach to the bottom of the screen, the
  lower end will be cut off about 30 pixel, so the window needs to be
  moved by the user each time to see the lower button row (e.g. settings
  dialog in netbeans on medium resolution screen).

  * In applications that save and restore window position and size, the
  window will move down 28 pixel each time it is opened an closed (e.g.
  JOSM, preference dialog).

  Expected behavior:

  * The result of getLocation() should be constant for one window unless
  the user moves the window

  * setSize(dx,dy) should not set the size of the content pane, but the
  size of the entire window, including window decorations

  * be consistent for all Window objects, e.g. in the attached sample,
  the JFrame works correctly, but the JDialog shows the described bug

  Output of the sample code (press button "click", then press button
  "click2"):

  dlg.getLocationOnScreen()=java.awt.Point[x=300,y=400]
  dlg.getLocationOnScreen()=java.awt.Point[x=301,y=428]

  Note: Both getLocation() and getLocationOnScreen() return the same
  values.

  Observed for the following Java versions:

  java version "1.6.0_24"
  OpenJDK Runtime Environment (IcedTea6 1.11.5) (6b24-1.11.5-0ubuntu1~12.10.1)
  OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

  and

  java version "1.7.0_09"
  OpenJDK Runtime Environment (IcedTea7 2.3.4) (7u9-2.3.4-0ubuntu1.12.10.1)
  OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)

  Ubuntu 12.10

  unity-6.12.0-0ubuntu0.2

  update: same behavior in gnome classic with compiz running

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