we just needed to find a problem that is very similar to yours.
Our findings: Java Webstart launches the creation of multiple EDT threads. If you start your applet as an application, there is only one EDT that would prevent the problem.
We could see activity on the second EDT only when we played with the console window (resize / hide). Resizing constantly made the problem reproducible very easily.
After a short hunt, we were able to find a place in our code where getGraphics is called in the drawing method. This triggered a chain of calls ending at the very top of all the components which appears to be shared with this console.
This probably happens when the application and the console are open, and the computer becomes unlocked by its user, since all components are redrawn simultaneously.
Hope this helps. I would be interested to know any further details about this common mistery component.
Personally, I would not suspect that the console uses a component with a main application that could block each other in this way.
Good luck.
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