So I looked at all the orders/admin confirmations that NEVER came through. They are for orders with a public email address (Yahoo, Hotmail, MSN)...the customer confirmations go out but the admin confirmation breaks down and does not go out for all orders made with a PUBLIC email address!
I think this issue may be due to the customer email address being used as the FROM address for the email to admin, which is interpreted in some way by the GoDaddy server as an attempt to send spam though your account. Try this:
Around line 2321 in ps_checkout.php find
$vendor_mail = vmMail( $shopper_email, $shopper_name, $vendor_email, $vendor_subject, $vendor_mail_Body, $vendor_mail_AltBody, true, null, null, $EmbeddedImages);
change to
$vendor_mail = vmMail( $from_email, $shopper_name, $vendor_email, $vendor_subject, $vendor_mail_Body, $vendor_mail_AltBody, true, null, null, $EmbeddedImages);
ie. $shopper_email is changed to $from_email
This puts the site admin as the FROM field so may get around this problem. This does mean that an admin cannot simply reply to the order email, but the customer email address is still shown in the order mail body.
ps_checkout.php is located in /administrator/components/com_virtuemart/classes/
The above code is in VM 1.1.9 today. But still to make it work I had to change also
in administrator\components\com_virtuemart\classes\ps_main.php around line 496
$mail->From = $from ? $from : $mosConfig_mail from;
$mail->Sender = $from ? $from : $mosConfig_mail from;
to
$mail->From = $mosConfig_mailfrom;
$mail->Sender = $mosConfig_mailfrom;
Seems to work now with SMTP and in the "from" field of a message to admin there is indeed admin's e-mail.
