Tane, Make sure that you put in the full local dev path instead of /admin/. So you can do something like:
$("input#ImageFilename").jqUploader({ src: '/js/jqUploader/jqUploader.swf', uploadScript: '<?php echo $html->url('/admin/images/ add/');?>', afterScript: '<?php echo $html->url('/admin/images/ add/');?>', background: 'FFFFDF', barColor: '64A9F6', allowedExt: 'jpg|JPG|jpeg|JPEG|png|PNG|gif|GIF' });