2nd time's a charm.  Seems I need the call in the constructor to
this.initDuration(); to get the apply method called:


/* ************************************************************************

   qooxdoo - the new era of web development

   http://qooxdoo.org

   Copyright:
     2008 1&1 Internet AG, Germany, http://www.1und1.de

   License:
     LGPL: http://www.gnu.org/licenses/lgpl.html
     EPL: http://www.eclipse.org/org/documents/epl-v10.php
     See the LICENSE file in the project's top-level directory for details.

   Authors:
     * Jonathan Weiß (jonathan_rass)

   ======================================================================

   This class contains code based on the following work:

   * script.aculo.us
       http://script.aculo.us/
       Version 1.8.1

     Copyright:
       (c) 2008 Thomas Fuchs

     License:
       MIT: http://www.opensource.org/licenses/mit-license.php

     Author:
       Thomas Fuchs

************************************************************************ */

/**
 * Combination effect "Pulsate"
 *
 * Fades the element in and out several times.
 */

qx.Class.define("qx.fx.effect.combination.Pulsate",
{

  extend : qx.fx.Base,

  /*
   
*****************************************************************************
       CONSTRUCTOR
   
*****************************************************************************
  */

  /**
   * @param element {Object} The DOM element
   */
  construct : function(element)
  {
    this.base(arguments, element);

    this.__fadeEffects = [
      new qx.fx.effect.core.Fade(element),
      new qx.fx.effect.core.Fade(element),
      new qx.fx.effect.core.Fade(element),
      new qx.fx.effect.core.Fade(element),
      new qx.fx.effect.core.Fade(element),
      new qx.fx.effect.core.Fade(element)
    ];

    this.initDuration();
  },


  /*
  
*****************************************************************************
      PROPERTIES
  
*****************************************************************************
   */

  properties :
  {

    /**
     * Number of seconds the effect should run.
     */
    duration :
    {
      init : 2,
      refine : true
    }

  },


  /*
  
*****************************************************************************
      MEMBERS
  
*****************************************************************************
   */

   members :
   {

    __oldValue : null,
    __fadeEffects : null,

    beforeSetup : function() {
      this.__oldValue = qx.bom.element.Style.get(this._getElement(),
"opacity");
    },


    start : function()
    {
      if (!this.base(arguments)) {
        return;
      }

      var counter = 0;
      var self = this;

      for (var i=0, l=this.__fadeEffects.length; i<l; i++)
      {
        this.__fadeEffects[i].id = counter;
        if (counter < 5)
        {
          this.__fadeEffects[i].afterFinishInternal = function(){
            self.__fadeEffects[this.id + 1].start();
          };
        }
        counter++;
      }
      this.__fadeEffects[0].start();
    },


    afterFinish : function() {
      qx.bom.element.Style.set(this._getElement(), "opacity",
this.__oldValue);
    },

    _applyDuration: function(value, old) {
      var effectDuration = value / 6;
      var counter = 0;

      for (var i=0, l=this.__fadeEffects.length; i<l; i++)
      {
        this.__fadeEffects[i].set({
          duration : effectDuration,
          to : ( (counter % 2) !== 0) ? 1 : 0,
          from : ( (counter % 2) !== 0) ? 0 : 1,
          transition: "sinodial",
          modifyDisplay : false
        });
        counter++;
      }
     }

   },


   /*
  
*****************************************************************************
      DESTRUCTOR
  
*****************************************************************************
   */

   destruct : function() {
     this._disposeArray("__fadeEffects");
   }
});

-- 
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