I have the HTML email module and it is working for most site emails, however those that are called by actions/triggers don't use the template. How I can I force this behaviour?
When you build an action on the settings page (/admin/config/system/actions) you have 2 options. One is 'send e-mail' and the other is 'send HTML e-mail'. 'Send e-mail' is plain text only, as where 'send HTML e-mail' allows the use of HTML templates. Make sure you are using the 'send HTML e-mail' action.