Right I believe I have found the cause of all this: Xinerama.

Xinerama is enabled on Gutsy but not on Feisty. The JNI native function
Java_sun_awt_X11GraphicsDevice_initXrandrExtension() is careful not to
use Xrandr if Xinerama is enabled. In sun/awt/X11GraphicsDevice.java the
overridden method getDisplayModes() calls its parent implementation
(which returns just the current display mode) if isFullScreenSupported()
returns false. isFullScreenSupported() returns false because
Java_sun_awt_X11GraphicsDevice_initXrandrExtension() skips using Xrandr
because of Xinerama.

So to get full screen mode working again we need to

  * See if Xrandr and Xinerama will work together safely and get the AWT code 
updated to support this in OpenJDK. I would presume any work of this size is 
unlikely to be back-ported to Java 6, so I guess it will be at least Java 7 
final before we could see this all working well again. I wonder if this work is 
already underway? I will send a mail to the awt-dev mailing list at OpenJDK to 
see if anything is happening.
  * In the meantime Xinerama could be disabled on machines which need to use 
full screen mode applications. I need to find out how this is done.

** Changed in: icedtea-java7 (Ubuntu)
       Status: New => Confirmed

** Changed in: sun-java6 (Ubuntu)
       Status: New => Confirmed

-- 
Java cannot change display modes / screen resolution in Gutsy
https://bugs.launchpad.net/bugs/154613
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