Cannot get this to work with user emails (registration/pass reset/etc)

Got the same problem.
Any suggestions..?

It seems like deleting all the tpl-files from the htmlmail-module solves this issue...
Am I right?

Have you added the custom tpl files to your theme and gone to admin/config/system/htmlmail to tell it which theme to search for the tpl files? It sounds like it's probably defaulting (falling back) to the unthemed htmlmail.tpl.php file, which is just printing out the $body variable.

You need to copy htmlmail.tpl.php into your theme. The you need to add something like htmlmail--user_register.tpl.php. Finally, you need to clear cache because the theme registry needs to be updated.

I solved this by deleting all the template files in the htmlmail module folder.

I think since the htmlmail module has a htmlmail--user--password_reset.tpl.php and htmlmail--user.tpl.php, it uses them instead of your template declared htmlmail.tpl.php.

If you don't want to hack the module, you'd have to explicitly re-declare those template files in your theme, so adding htmlmail--user--password_reset.tpl.php and htmlmail--user.tpl.php in your theme folder. That's really lame and messy if you want just one template for all your emails though.