I have come up with some code to add functionality to the Batch Issues command.  Sometimes, I want to choose specific issues from a filter instead of filtering the data first.  I added 2 things.  The first is an input object to handle the checkbox click, the second is javascript to uncheck/check the items in a checkboxlist.

Here is how you do it:

Add this code after line 17

....
<script language="javascript" src="../DCheck.js"></script>

<script language="JavaScript">
<!--
   function readListControl()
   { 
      var objSelectAll = document.getElementById('chkSelectAll'); 
      var objSpan = document.getElementById('chklstIssues'); 
      for (var j=0; j<objSpan.childNodes.length; j++)
      {
         var objCurrentControl = objSpan.childNodes[j]; 
         if (objCurrentControl.id != null) 
            objCurrentControl.checked = objSelectAll.checked;
      }
   }
// -->
</script>
..

....
<tr>
   <td height="100%" vAlign="top" align="center">
      <input type="checkbox" id="chkSelectAll" checked onclick='readListControl()' /> Check/Uncheck All<br /><br />
      <TABLE id="Table1" cellSpacing="0" cellPadding="5" align="center" border="0" height="100%">
         <tr>
            <td valign="top">
               <asp:CheckBoxList id="chklstIssues" runat="server" Width="100%" Font-Size="Smaller" RepeatLayout="Flow"></asp:CheckBoxList>
            </td>
         </tr>
      </TABLE>
....

Hope this helps out!

~S