It seems that some changes introduced to Java 7 cause that stereo is not working. The same code using Canvas3D from Harvey's Java3D 1.6.0-pre9 works properly on JRE 1.6 and on JRE 1.7 only one eye is rendered.

This was tested on platform: Linux 64-bit + Nvidia Quadro 6000 + 331.38 driver + current JOGL + Java 3D 1.6.0-pre9


Example code:
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import com.sun.j3d.utils.geometry.ColorCube;
import com.sun.j3d.utils.universe.SimpleUniverse;
import java.awt.BorderLayout;
import java.awt.GraphicsConfiguration;
import java.awt.GraphicsEnvironment;
import javax.media.j3d.BranchGroup;
import javax.media.j3d.Canvas3D;
import javax.media.j3d.GraphicsConfigTemplate3D;
import javax.media.j3d.Shape3D;
import javax.media.j3d.View;
import javax.swing.JFrame;

public class Java3DTest {

    public static void main(String[] args) {
        GraphicsConfigTemplate3D template = new GraphicsConfigTemplate3D();
        template.setStereo(GraphicsConfigTemplate3D.REQUIRED);
        GraphicsConfiguration gcfg
                = GraphicsEnvironment.getLocalGraphicsEnvironment().
                getDefaultScreenDevice().getBestConfiguration(template);
        final Canvas3D canvas = new Canvas3D(gcfg);
        canvas.setStereoEnable(true);        

        JFrame frame = new JFrame("test frame");
        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        frame.setBounds(0, 0, 640, 480);
        frame.setLayout(new BorderLayout());
        frame.add(canvas, BorderLayout.CENTER);
        frame.setVisible(true);
                
        SimpleUniverse universe = new SimpleUniverse(canvas);
        View view = canvas.getView();

        BranchGroup scene = new BranchGroup();
        Shape3D shape = new ColorCube(0.5);
        scene.addChild(shape);
        universe.addBranchGraph(scene);
        universe.getViewingPlatform().setNominalViewingTransform(); 
    }