I am attempting to make a custom template for my Commerce Email emails. CE uses Variable Email and HTMLMail. I have put the template (named htmlmail--variable_email--custom_email_order.tpl.php) into the root of my theme folder. Nothing. The test htmlmail template is in the same place and works fine. I have cleared caches on the performance and in PHPMyAdmin, and run cron. Still doesn't work. Is this peculiar to Variable Email or HTMLMail?
It's not enough to leave the theme selection entry as Current theme; you must explicitly state that you want to use the theme you are already using. Now everything works.