FULL PRODUCT VERSION :
java version "1.6.0_06"
Java(TM) SE Runtime Environment (build 1.6.0_06-b02)
Java HotSpot(TM) Client VM (build 10.0-b22, mixed mode, sharing)


ADDITIONAL OS VERSION INFORMATION :
Any Linux distribution. For example:
Linux greyswan 2.6.24-19-generic #1 SMP Fri Jul 11 23:41:49 UTC 2008 i686 GNU/Linux

EXTRA RELEVANT SYSTEM CONFIGURATION :
Compiz  or other composition manager turned on (which is a default option for modern distributions). This happens even if "Java workarounds" are turned on in Compiz.

A DESCRIPTION OF THE PROBLEM :
- Sometimes blank screens appear.
- Sometimes the screens are only partially blank and there is a place where a part of them is visible. Resizing the window does not increase that part.
- Sometimes the size of the window is obviously incorrect (too big or too small).
- Sometimes the screens are not visible at all (but still they receive focus and can be manipulated in a blind manner).

The bug reproduces on any Linux with Compiz. The effects do not happen every single time, but still they are too often.


==================================================================
THIS BUG IS KNOWN FOR AGES:
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6429775
IT IS NOT FIXED YET, however, its status was set to "10-Fix Delivered".

See the last comment in that report: "This bug is 2 years old and it's still not fixed :(
Sun, please, just fix it, we all really need it."
==================================================================

Now regarding the "workaround":
AWT_TOOLKIT=MToolkit

This workaround is NOT an option. While the windows begin to appear, the keyboard does not work.
For instance, in Netbeans 6.1the shortcuts and keypresses like "Delete" or "Alt+Shift+O" do not work in UML editor. There are lots of other places where keyboard stop working.

The same problems are visible in software like IntelliJ Idea. Without workaround the windows are not painted properly, but with it there are problems with keyboard.

==================================================================

I do not think this bug is a fault of Compiz. Because if it would be, the rest of applications would suffer too. It is only Java programs which can not paint themselves correctly.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Set up any modern Linux distribution (like Ubuntu 8.04).
Set up java 6 there and any Java software which has GUI (like Netbeans 6.1).
Run that software for sometime opening various windows (including dialogs).

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
The windows (including dialogs) should have been painted correctly.
ACTUAL -
Sometimes windows are not painted or even not shown at all. Sometimes they have incorrect size.

REPRODUCIBILITY :
This bug can be reproduced often.

CUSTOMER SUBMITTED WORKAROUND :
There is no working workaround.
Forget about AWT_TOOLKIT=MToolkit, it's a fake.