Let me try 
This is the custom field:
When I receive a new order I manually fill out the field with some Ticket-info to the customer.
Then when I change the order to confirmed, they get an email with this text along with the order info.
So far so good!
But when the pay with creditcard, this text isn't in the email.
I do the same thing, after I get the order, I manually add the text to the custom field.
Then I head over to capture the payment, in this case QuickPay - Quickpay then sets the order in HikaShop to confirmed and the customer gets the above email, but without the text from the custom field.
I assume the confirm emails are the same wether offline payment or card payment?