Custom Fields appearing in admin notifications but not customer notifications

Hi,

Please check the display settings of your custom fields. They have specific display settings for each email so it's possible to disable their display for some emails and not others.
Also, it could well come from an override of the emails if they are from before HikaShop 3.
You have such line in the preload of the emails which loads the custom fields allowed to be displayed with the name of the email:
$fields = $fieldsClass->getFields('display:mail_order_creation=1',$data->cart,'order','');
Before HikaShop 3, you didn't had different options for different emails and thus the part 'display:mail_order_creation=1' was different and it's not compatible with the new options.