Please read the posts about this. filterGrid currently is not fully supported on the header grid.

<table id="organizations" class="scroll" cellpadding="0" cellspacing="0"></table><br/>
 <div id="organizations_pager" class="scroll" style="text-align:center;"></div><br/>

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code as follow: (notice that I used recommended gridModel:true,gridNames:false,gridToolbar:true)

organizationGrid = $("#organizations").jqGrid({
   url:"/intranet/organization/list?nd="+new Date().getTime(),
   editurl: "/intranet/organization/edit",
   datatype: "json",
   colNames:["Id", 
        "organization",
        "phone",
        "last name",
        "first name",
        "title",
        "email",
        "actions"],
   colModel:[{name:"organization_id", index:"organization_id", width:10, hidden:true},
        {name:"name", index:"name", width:300},
        {name:"phone_number", sortable:false, width:80},
        {name:"last_name", index:"last_name", width:100},
        {name:"first_name", index:"first_name", width:100},
        {name:"title", index:"title", width:200},
        {name:"email", sortable:false, width:80},
        {name:"actions", sortable:false, width:54, align:"center"} ],
   sortname: "<?php echo $this->sidx; ?>",  /* default: name  */
   sortorder: "<?php echo $this->sord; ?>", /* default: asc   */
   rowNum:<?php echo $this->rows; ?>,    /* default: 5    */
   page:<?php echo $this->page; ?>,     /* default: 1    */
   pager: $("#organizations_pager"),
   viewrecords: true,
   imgpath: img_path,
   rowList:[5,10,25],
   altRows: true,
   toolbar: [true,"top"]
    }); //end organization grid
  jQuery("#t_organizations").height(25).hide().filterGrid("organizations",{gridModel:true,gridNames:false,gridToolbar:true});
  jQuery("#organizations").navGrid('#organizations_pager',
   {edit:false,add:false,del:false,search:false,refresh:true}).navButtonAdd("#organizations_pager",
   {caption:"",title:"Toggle Search",buttonimg: img_path + "find.gif",
   onClickButton:function(){
    if(jQuery("#t_organizations").css("display")=="none") {
     jQuery("#t_organizations").css("display","");
    } else {
     jQuery("#t_organizations").css("display","none");
    } 
   }
  });