Reported at http://mail.openjdk.java.net/pipermail/awt-dev/2013-April/004619.html

I'm using in my application fullscreen mode. Since 1.6 java have a lot of
issue with it I using X11 native binding for it.
Use JNA 3.4. To going to fullscreen I send XSendEvent as _NET_WM_STATE with
_NET_WM_STATE_FULLSCREEN

You can look at test application on the github:
https://github.com/vkravets/FullScreenTest. Main Class: Main or MinTest

So about the issue... I have an issue with modal dialogs or windows which I
try to show when my main window in fullscreen mode.
>From 1.7 java is not working as expected. In 1.6 java modal dialogs/windows
appeared above fullscreen window as it should be, but in 1.7 and 1.8 all
modal dialogs/windows appeared under the fullscreen window.

I'm using wm Metacity, the same I have noticed on Gnome Shell... It seems
that it's related to all clones of Metacity...

I'm try to see how it's perform by defult native frameworks and I tested
GTK3 and SWT which is using GTK bindings. And everything is working as
expected. SmartGit which written on Java and use SWT don't have such
problem. VLC/GTK the same - in fullscreen mode I can call some dialogs
which will be appeared above fullscreen window.

It's very strange  for me that Java in own documentation have such lines:
Quote from GraphicsDevice#setFullScreenWindow:
"
Windows cannot overlap the full-screen window. All other application
windows will always appear beneath the full-screen window in the Z-order.
"

Since from 1.7 java is using the same message _NET_WM_STATE with
_NET_WM_STATE_FULLSCREEN to going to fullscreeb and is not clear why we
have such broken behavior with modal dialogs from 1.7 java and such lines
in the documentation....