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The problem can lie with the hierarchy of the application and can require additional research to discover what could be the conflict stopping this class being seen. What seems to happen is that with the hierarchy of the java application there is a class which is not visible when show all classes not enabled, which stops the class you require being shown.
You will have to go through the javaex.ini file one class at a time, setting it to TRUE to discover the offending class and then setting this to TRUE in conjunction with the class that you want to test. Once this is done, you can then view the class you require to test with ShowAllClasses set to FALSE.