This problem is seen on an application which uses several Swing/AWT windows on a multi-head display. The customer typically starts up 3 instances of their application and puts one instance in each screen. When they do something un-related to the application, such as bringing up Windows Explorer, the entire Java application repaints, causing the screen to flicker and a very unpleasant visual effect for their users.
The customer is using 1.4.0_01 and 1.4.0_03 on Windows 2000 SP2. Other Windows platforms have not been tested. The application typically runs on a system with 3 monitors and a multi-head grahics card, such as the Matrox G200 MMS (2,4) 32 MB. The problem can be seen with a single display, but it is not nearly as obvious or reproducible.
A stack trace taken by the customer at the time of a repaint is attached.