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It looks like a problem in your Java or environment settings and not like a problem of the simulator. Have you tried other Java GUIs? I think they will behave similarly.
Nevertheless, to work with the simulator without solving the problem, using the setLocation method of the frame is a good idea. To use all windows you should set the method in all of the following classes:
These are all graphical user interfaces which should appear during a normal simulation. But for solving the intial problem you should look at your environment and test other java programs.