Your problem is that you're unknowingly adding the layout to both the JFrame and its contentPane. The solution is to make sure you add it to the JFrame's contentPane only:
GroupLayout alternateGUILayout = new GroupLayout(alternateGUIFrame.getContentPane());
alternateGUIFrame.getContentPane().setLayout(alternateGUILayout);
It's the first line above that matters the most.
Another option is to work with JPanels, and then add the JPanels to the JFrame's contentPane in its default BorderLayout.CENTER position.