CKeditor doesn't format the body value
According to my experience &lt;br&gt; causes this problem ,my solution for this is to replace all &lt;br&gt; with &lt;br /&gt;  before saving in body field 

So try 

$body =   str_replace("&lt;br\s*&gt;", "&lt;br /&gt;",nl2br($item-&gt;body_value));