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Repro: create JFrame with border layout. In the center pane put a JScrollPane. Put a JTable in the JScrollPane. In the north pane put a JComboBox. Right click on the JFrame on the Form node in the project navigator. Select "Set Layout". The layout sub menu doesn't post--instead there's a small square with side length a millimeter or so. Right clicking on the JFrame in the form editor yields the same small square. Right clicking on other components appears to work correctly.
Created attachment 30426 [details] Screen shot of problem
I am sorry, I am not able to reproduce this issue. Could you, please, provide more details. What JDK do you use? Is your problem 100% reproducible or it occurs occasionally? What component is focused before you right-click on the JFrame? Etc.
Created attachment 30917 [details] Screenshot of the problem
Finally I was able to reproduce this issue. I overlooked that the reporter selects the node in the _Projects_ window, not in the Inspector. The problem is that the selection in the GUI designer is determined by the selection in the designer area or by the selection in the Inspector window. The Projects window also shows the form nodes, but the selection is not tracked there. There is more problems caused by this fact. I would recommend to remove these nodes from the Projects window because they are misleading and we probably are not able to ensure that all actions will work correctly there.
This is no longer an issue - in 6.0 Projects/Files view no longer shows subnodes of files (Navigator/Inspector used instead).