FULL PRODUCT VERSION :
Java(TM) SE Runtime Environment (build 1.6.0-rc-b94)


A DESCRIPTION OF THE PROBLEM :
JLayeredPane will turn off optimized drawing if it contains components in layers that are not:
1. In the FRAME_CONTENT_LAYER
2. A JInternalFrame
3. Or the layer property is null.

code from JLayeredPane that determines this:
    private void validateOptimizedDrawing() {
        boolean layeredComponentFound = false;
        synchronized(getTreeLock()) {
            Integer layer = null;

            for (Component c : getComponents()) {
                layer = null;
                JComponent jc = (JComponent)c;
                if(c instanceof JInternalFrame || (c instanceof JComponent &&
                         (layer = (Integer)((JComponent)c).getClientProperty(
                          LAYER_PROPERTY)) != null)) {
                    if(layer != null && layer.equals(FRAME_CONTENT_LAYER))
                        continue;
                    layeredComponentFound = true;
                    break;
                }
            }
        }
        
        if(layeredComponentFound)
            optimizedDrawingPossible = false;
        else
            optimizedDrawingPossible = true;
      }
---------------------
A problem occurs when the user defines a layer in the FRAME_CONTENT_LAYER and in the DEFAULT_LAYER. The setting of layers appears to always happen for layers except for the DEFAULT_LAYER:
   public void setLayer(Component c, int layer, int position) {
        Integer layerObj;
        layerObj = getObjectForLayer(layer);
        if(layer == getLayer(c) && position == getPosition(c)) {
                repaint(c.getBounds());
            return;
        }
        /// MAKE SURE THIS AND putLayer(JComponent c, int layer) are SYNCED
        if(c instanceof JComponent)
            ((JComponent)c).putClientProperty(LAYER_PROPERTY, layerObj);
        else
            getComponentToLayer().put((Component)c, layerObj);
        
        if(c.getParent() == null || c.getParent() != this) {
            repaint(c.getBounds());
            return;
        }

        int index = insertIndexForLayer(c, layer, position);

        setComponentZOrder(c, index);
        repaint(c.getBounds());
    }
----------------
In this case, the process short circuits because getLayer will return DEFAULT_LAYER if there isn't a layer set and the targeted layer is the DEFAULT_LAYER. The result is that JComponents in the JLayeredPane from the DEFAULT_LAYER will never play into turning off of optimized drawing. Im not sure what the rationale is here given that components can still overlap in the same layer which would violate the contract for isOptimizedDrawingEnabled:
Returns false if components in the pane can overlap, which makes optimized drawing impossible. Otherwise, returns true.

Why not have it return false when any component does not reside in the FRAME_CONTENT_LAYER or is a JInternalFrame?


STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run this code, notice how the layer the component resides in affects the drawing process:
import javax.swing.*;
import javax.swing.border.*;
import java.awt.*;

public class ShowJLayeredProblem implements Runnable{

    public static void main(String ... args){
SwingUtilities.invokeLater(new ShowJLayeredProblem());
    }

    public void run(){
        JFrame jf = new JFrame();
        JPanel jp = new JPanel();
        GridLayout gl = new GridLayout(1,2);
        jp.setLayout(gl);
        JLayeredPane jlp = new JLayeredPane();
        jlp.setBorder(new TitledBorder("FRAME_CONTENT_LAYER and DEFAULT_LAYER"));
        TwoComponentLayoutManager tclm = new TwoComponentLayoutManager();
        JButton jb = new JButton("One");
        jlp.add(jb, jlp.FRAME_CONTENT_LAYER);
        tclm.one = jb;
        JButton jb2 = new JButton("Two");
        jlp.add(jb2, jlp.DEFAULT_LAYER);
        tclm.two = jb2;
        jlp.setLayout(tclm);
        jp.add(jlp);

        JLayeredPane jlp2 = new JLayeredPane();
        jlp2.setBorder(new TitledBorder("-1000 and -1001"));
        TwoComponentLayoutManager tclm2 = new TwoComponentLayoutManager();
        JButton jb12 = new JButton("One");
        jlp2.add(jb12, new Integer(-1000));
        tclm2.one = jb12;
        JButton jb22 = new JButton("Two");
        jlp2.add(jb22, new Integer(-1001));
        tclm2.two = jb22;
        jlp2.setLayout(tclm2);
        System.out.println(jlp2.isOptimizedDrawingEnabled());
        jp.add(jlp2);

        jf.add(jp);
        jf.setSize(1000,1000);
        jf.setVisible(true);
    }


    static class TwoComponentLayoutManager implements LayoutManager2{
        Component one;
        Component two;
        public void addLayoutComponent(Component comp, Object constraints){
            Integer i = (Integer)constraints;
            if(i.equals(one)) one = comp;
            else two = comp;
        }

        public float getLayoutAlignmentX(Container target){
            return 1.0f;
        }

        public float getLayoutAlignmentY(Container target){
            return 1.0f;
        }

        public void invalidateLayout(Container target) {}

        public Dimension maximumLayoutSize(Container target) { return new Dimension(Integer.MAX_VALUE, Integer.MAX_VALUE); }
        public Dimension preferredLayoutSize(Container target){ return new Dimension(0,0); }
        public Dimension minimumLayoutSize(Container target){ return new Dimension(0,0); }

        public void addLayoutComponent(String s, Component c){}
        public void removeLayoutComponent(Component c){}
        public void layoutContainer(Container target){
            Insets i = target.getInsets();
            Dimension size = target.getSize();
            int w = size.width/2;
            int h = size.height/2;
            one.setBounds(i.left,i.top, w,h);
            two.setBounds(w/2,h/2,w,h);

        }


    }



}

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
That the 2nd button be always on top, optimized drawing disabled
ACTUAL -
The 2nd button can be below the 1rst, optimized drawing enabled

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
import javax.swing.*;
import javax.swing.border.*;
import java.awt.*;

public class ShowJLayeredProblem implements Runnable{

    public static void main(String ... args){
SwingUtilities.invokeLater(new ShowJLayeredProblem());
    }

    public void run(){
        JFrame jf = new JFrame();
        JPanel jp = new JPanel();
        GridLayout gl = new GridLayout(1,2);
        jp.setLayout(gl);
        JLayeredPane jlp = new JLayeredPane();
        jlp.setBorder(new TitledBorder("FRAME_CONTENT_LAYER and DEFAULT_LAYER"));
        TwoComponentLayoutManager tclm = new TwoComponentLayoutManager();
        JButton jb = new JButton("One");
        jlp.add(jb, jlp.FRAME_CONTENT_LAYER);
        tclm.one = jb;
        JButton jb2 = new JButton("Two");
        jlp.add(jb2, jlp.DEFAULT_LAYER);
        tclm.two = jb2;
        jlp.setLayout(tclm);
        jp.add(jlp);

        JLayeredPane jlp2 = new JLayeredPane();
        jlp2.setBorder(new TitledBorder("-1000 and -1001"));
        TwoComponentLayoutManager tclm2 = new TwoComponentLayoutManager();
        JButton jb12 = new JButton("One");
        jlp2.add(jb12, new Integer(-1000));
        tclm2.one = jb12;
        JButton jb22 = new JButton("Two");
        jlp2.add(jb22, new Integer(-1001));
        tclm2.two = jb22;
        jlp2.setLayout(tclm2);
        System.out.println(jlp2.isOptimizedDrawingEnabled());
        jp.add(jlp2);

        jf.add(jp);
        jf.setSize(1000,1000);
        jf.setVisible(true);
    }


    static class TwoComponentLayoutManager implements LayoutManager2{
        Component one;
        Component two;
        public void addLayoutComponent(Component comp, Object constraints){
            Integer i = (Integer)constraints;
            if(i.equals(one)) one = comp;
            else two = comp;
        }

        public float getLayoutAlignmentX(Container target){
            return 1.0f;
        }

        public float getLayoutAlignmentY(Container target){
            return 1.0f;
        }

        public void invalidateLayout(Container target) {}

        public Dimension maximumLayoutSize(Container target) { return new Dimension(Integer.MAX_VALUE, Integer.MAX_VALUE); }
        public Dimension preferredLayoutSize(Container target){ return new Dimension(0,0); }
        public Dimension minimumLayoutSize(Container target){ return new Dimension(0,0); }

        public void addLayoutComponent(String s, Component c){}
        public void removeLayoutComponent(Component c){}
        public void layoutContainer(Container target){
            Insets i = target.getInsets();
            Dimension size = target.getSize();
            int w = size.width/2;
            int h = size.height/2;
            one.setBounds(i.left,i.top, w,h);
            two.setBounds(w/2,h/2,w,h);

        }


    }



}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
don't use DEFAULT_LAYER