Hi there, 

I believe, the simplest and quickest way of fixing that top-level-skin problem is replacing the doSkin method of class
org.apache.jetspeed.modules.actions.portlets.CustomizeSetAction with the code displayed below. 
It simply does not allow to set null skin reference for top PSML element, 
replacing null with default skin, when necessary. I already use this fix in my company's jetspeed-based portal.

Regards
Olaf Romanski, olaf.romanski@tpg.pl

    /**
     * Set the skin in the PSML and the current PortletConfig
     * using the HTML parameter "skin".  If the parmeter is
     * missing or 'blank', then the skin is set to null.
     *
     */
    public void doSkin(RunData rundata, Context context)
    {
        // we should first retrieve the portlet to customize and its parameters
        // definition
        PortletSet set = (PortletSet) ((JetspeedRunData) rundata).getCustomized();
        
        try
        {            
            String skin = rundata.getParameters().getString("skin");
            Profile profile = ((JetspeedRunData) rundata).getCustomizedProfile();
            Portlets portlets = profile.getDocument().getPortletsById(set.getID());
            
            // skin is neither null nor zero-length
            if ((skin != null) && (skin.trim().length() > 0))
            {
                PortletSkin s = PortalToolkit.getSkin(skin);

                if (s != null)
                {
                    set.getPortletConfig().setPortletSkin(s);

                    Skin psmlSkin = portlets.getSkin();
                    if (psmlSkin == null)
                    {
                        portlets.setSkin(new PsmlSkin());
                    }
                    portlets.getSkin().setName(skin);
                }
                else
                {
                    Log.warn("Unable to update skin for portlet set " 
                             + set.getID() + " because skin " + skin 
                             + " does not exist.");
                    return;
                }
            }
            else
            {
              // skin is either null or zero-length
              String custPortletSetID = portlets.getId();
              String rootPortletSetID = profile.getRootSet().getID();
              
              // set system default skin for root PSML element
              if (custPortletSetID != null && rootPortletSetID != null &&
                  custPortletSetID.equals(rootPortletSetID))
              {
                // get system default skin
                String defaultSkinName = JetspeedResources.getString("services.PortalToolkit.default.skin");
                PortletSkin defaultSkin = PortalToolkit.getSkin(defaultSkinName);
                
                if (defaultSkin != null)
                {
                  set.getPortletConfig().setPortletSkin((PortletSkin) defaultSkin);
                  Skin psmlSkin = portlets.getSkin();
                  
                  if (psmlSkin == null)
                  {
                    portlets.setSkin(new PsmlSkin());
                  }
                
                  portlets.getSkin().setName(defaultSkin.getName());
                }
                else
                {
                    Log.warn("Unable to set default skin for root portlet set " 
                             + set.getID() + " because skin " + skin 
                             + " does not exist.");
                    return;
                }
              }
              else
              {
                // By setting the skin to null, the parent's skin will be used.
                set.getPortletConfig().setPortletSkin((PortletSkin) null);
                portlets.setSkin(null);
              }
            }
        }
        catch (Exception e)
        {
            Log.error(e);
        }        
    }