Hi,
Thanks for the information. Let's continue.
1. One possible reason this would happen would be if the comment was added to the order after the order was created. In that case, it would be normal that these emails do not contain the comment since they are sent when the order is created, and not when it is updated.
Could you provide a screenshot of the "history" section of that particular order (you can see it at the bottom of the page when you edit an order via the orders listing in the backend).
2. Could you also provide the PHP code used by harmis to create the order and add to it the comment custom field so that we can better understand what is happening ?
3. One thing you could try is to add the tag {VAR:order.comment} to the HTML of these emails. That will force the display of the content of the custom field in the email, regardless of the display options and restrictions of the custom field. So if the tag is replaced by nothing when the order is created by harmis, it will confirm that the order is created without the custom field provided and that its value is added afterwards, when these emails are already sent. That would explain why the preview on these emails for that order works fine but not the email sent when harmis creates the order.