Well, here is a "small" test case:
// LWJGLProblem.java
import org.lwjgl.LWJGLException;
import org.lwjgl.opengl.AWTGLCanvas;
import org.lwjgl.opengl.PixelFormat;
import java.awt.*;
import javax.swing.*;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import static org.lwjgl.opengl.GL11.*;
public class LWJGLProblem extends JFrame implements ChangeListener{
private JSlider slider = new JSlider();
private MyCanvas canvas;
/**
* Creates a new LWJGLProblem
*/
public LWJGLProblem(){
setSize(640, 480);
setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
setLayout(new BorderLayout());
add(slider, BorderLayout.NORTH);
try{
canvas = new MyCanvas();
add(canvas, BorderLayout.CENTER);
}catch(LWJGLException e){
e.printStackTrace();
}
slider.addChangeListener(this);
}
/**
* Called when the slider moves
* @param e The event data
*/
public void stateChanged(ChangeEvent e){
canvas.repaint();
}
/**
* Starts the program :)
* @param args The program arguments
*/
public static void main(String[] args){
LWJGLProblem frame = new LWJGLProblem();
frame.setVisible(true);
}
/**
* This is the AWTGLCanvas the will show the preview
* @author Tim Steenwyk
*/
private class MyCanvas extends AWTGLCanvas{
/**
* Creates a new Canvas
* @throws LWJGLException If we can't make a view
*/
public MyCanvas() throws LWJGLException{
super(new PixelFormat(8, 16, 0));
}
/**
* Initializes OpenGL for the preview
*/
public void initGL(){
glClearColor(0.0f, 0.0f, 0.0f, 1.0f);
glDisable(GL_LIGHTING);
glDisable(GL_DEPTH_TEST);
glDepthMask(false);
glEnable(GL_SCISSOR_TEST);
glEnable(GL_BLEND);
glEnable(GL_TEXTURE_2D);
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
glTexEnvi(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_MODULATE);
}
/**
* Paints the preview
*/
public void paintGL(){
int width = getWidth();
int height = getHeight();
glClearColor((float)Math.random(), (float)Math.random(), (float)Math.random(), 1.0f);
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
glViewport(0, 0, width, height);
glScissor(0, 0, width, height);
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
glOrtho(0.0, width, height, 0.0, -1.0, 1.0);
glMatrixMode(GL_MODELVIEW);
glLoadIdentity();
glColor4f(1.0f, 0.0f, 0.0f, 0.4f);
glDisable(GL_TEXTURE_2D);
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
glBegin(GL_QUADS);
drawRectangle(5, 15, 108, 50);
drawRectangle(15, 25, 108, 50);
drawRectangle(25, 35, 108, 50);
drawRectangle(35, 45, 108, 50);
drawRectangle(45, 55, 108, 50);
glEnd();
if(glGetError() != GL_NO_ERROR){
System.out.println("whoops");
}
try{
swapBuffers();
}catch(LWJGLException e){
e.printStackTrace();
}
}
/**
* Draws a rectangle having the specified parameters
* @param x The x location
* @param y The y location
* @param width The width of the rectangle
* @param height The height of the rectangle
*/
private void drawRectangle(float x, float y, float width, float height){
glVertex2f(x, y);
glVertex2f(x, y + height);
glVertex2f(x + width, y + height);
glVertex2f(x + width, y);
}
/**
* Handles errors that were thrown during a paint
* @param exception The exception that was thrown
*/
protected void exceptionOccurred(LWJGLException exception){
exception.printStackTrace();
}
}
}
Another strange thing is that today it seems to stop drawing everything, including the clear color.
Just move the slider back and forth for a while and it should stop drawing.
Hope you guys can reproduce it

By the way, here are my system specs if you need them:
Windows XP Pro SP2, Intel Core 2 Duo 6600, Nvidia Geforce 7950GT, 2GB ram
All drivers/patches are up-to-date
EDIT: I'm using Java v6.0