Please run the following example:

import java.awt.*;
import java.awt.event.*;
import javax.swing.*;

public class Test {

    public static void main(String args[]) {
        try {
            final int size = 200;
            SwingUtilities.invokeAndWait(new Runnable() {
                public void run(){
                    JFrame frame = new JFrame("test");
                    frame.getContentPane().setBackground(Color.red);
                    frame.setSize(size, size);
                    frame.setUndecorated(true);
                    frame.setVisible(true);
                    frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
                }
            });
        } catch (Exception e) {
            System.err.println(e.getMessage());
        }
    }
}

expected: reb BG for the frame (checked on Ubuntu 14.04 Linux + JDK9 b93)

HiDPI + Ubuntu 15.04 + GNOME (3.14.4) + same JDK: BG isn't red (checked both scaling-factors 1 and 2).