I've had to deal with remoting upgrading several machines to Java 7 and FMS12v4. And one of the annoying things on a Mac server is that using the Screen App to connect into the server, which uses VNC, gives you blank (white) Java screens that you can't do anything with. I used to do thing like dragging the window mostly off screen and bringing it back and it would then refresh and I could see it. But it was very unpredictable. However, today I found out that if I minimize the Java window (e.g., hit the yellow button in the top left of the Java window), it will go down into the dock. When I then click on it in the dock, it will open up refreshed with all of the Window contents.
This is only a problem if you remote into a Mac server. If you work direclty on the server, it will display the Java window contents. But just remember to minimize and then expand and it will fix Java redraw problems.