What is wrong with the counter? What is it, that it is (or is not) doing, that is not what you want, and what is it that you want?
I appears to me that it is increasing by increments of 5 when a block it hit.
public void gameOver()
{
JOptionPane.showMessageDialog(null," You lost, nonetheless you've made a mess and has disrupted E=M(C^2)");
Counter counter = (Counter) getWorld().getObjects(Counter.class).get(0);
getWorld().addObject(new ScoreBoard(counter.getValue() ), getWorld().getWidth()/2, getWorld().getHeight()/2);
Greenfoot.delay(180);
backgroundMusic.pause();
Greenfoot.playSound("applause.wav");
Greenfoot.setWorld(new Over());
}