Not sure if there is other cases where this may apply but on a server using WHM email can be set to be sent through the main IP instead of the IP the domain is hosted on. When sending email from domain of different IP than the main IP if the -f parameter is not included with the sendmail function the Return-Path for email is set to the hostname and could hamper delivery of email.

Setting the -f parameter on line 650 of includes/functions_messenger.php will produce the correct return path.

$result = $config['email_function_name']($to, mail_encode($subject, ''), wordwrap(utf8_wordwrap($msg), 997, "\n", true), $headers, "-f" . $config['board_email']);

I realize this could also be considered WHM bug but given the popularity of WHM and Cpanel I would suggest this should at very least be option under email settings.