well html in emails is being done by you in your translations it would appear. None of our default emails in phrases.php have break html tags we use /n and /r in them not html.
I also wonder why as I have tested the default email and it works why only half your variables work in the email. Look at your email some variables are correct others are not.
This is a default message it looks like emailreply
Code:
Content visible to verified customers only.
Based on that email we then apply the replacements below.
Code:
Content visible to verified customers only.