Thanks for the file, I think that I can see the problem, it looks like the page that was used for the message was originally a template. It seems that the template declarations are coded with js script possibly. If you can post back with the page the email body was derived from I might be able to see why it was set like this.
To fix it try updating line 47 in waue_upload_files_1.php to be like this instead:
$MailBody = $MailBody . "<!-- In\"+\"stanceEndEditable --><!-- In\"+\"stanceEndEditable --></body> <!-- In\"+\"stanceEnd --><!-- In\"+\"stanceEnd --></html>";
Let us know how this works for you.