Whole screen is not repainted, need debug tips

Question

We are running an application which uses some jogl for animaties.
Sometimes when the animation is finished and we set the GLCanvas to invisible, the normal
java JPanels are not repainted.
Also alt-tab to another windows application and back will not force a redraw.
The application itself is still working, clicking on a (now) not visible button will trigger
the jogl animations, and these are show correctly.
Also from logging it appear that the AWT-thread is not blocking.
We are looking for tips that can help find us the problem from logging
as it only appears a few times a week and it is not reproducable.

Answer 1

The problem is that most of the time it works, but after some hours/days, the java panels are not repainted.
There is no memory leak.
paintComponent is not overwritten, a object is made visible to do the animation.
Pseudo code:
public class AnimateTilePopup extends JPanel {
GLCanvas glCanvas;
public AnimateTilePopup() {
super(null);
setOpaque(true);
glCanvas = new GLCanvas();
glCanvas.setLocation(0,0);
glCanvas.setSize(width, height);
glCanvas.setVisible(false);
glCanvas.setFocusable(false);
add(glCanvas);
flipRendererZoom = new AnimateRendererZoom();
glCanvas.addGLEventListener(flipRendererZoom);
public startAnimation() {
glCanvas.setVisible(true);
this.setVisible(true);
public stopAnimation() {
glCanvas.setVisible(false);
this.setVisible(false);
So sometimes when we call stopAnimation(), the animation is stoppped, but the underlying java JPanels are not repainted.
When we now call startAnimation, the animation is shown and when stopped, no repaint for the normal JPanels.
Most times it is working perfectly, only sometimes it failes.
What can be the cause or what logging can be gather that might gives us a clue how to fix this problem.