I have taken a look and your code is OK in fckplugin.js inside the folder equation_html, but is different in the same file inside the folder equation:

else if (window.focus) 
{ 
  //popupEqnwin.focus();
	if(latex!==undefined)
	{
	eq = eq.replace(/\\/g,'\\\\');
      eq = eq.replace(/'/g,'\\'');
      eq = eq.replace(/"/g,'\\"');
      eq = eq.replace(/0/g,'\\0');
 
	eval("var old = popupEqnwin.document.getElementById('JSONload')");
	if (old != null) {
		old.parentNode.removeChild(old);
		delete old;
}
(...)

I have downloaded both files from your page ( http://www.codecogs.com/pages/functions/download.php?dir=/latex/integration/fckeditor~8a00af5ae3&file=fckplug

Configuring the editor with equation_html works fine. Thanks a lot.