I see that the Mail Template settings are set to HTML.
But I just created a new account and still have the same issue:
Hello {NAME},
Thank you for registering at {SITENAME}. Your account is created and must be activated before you can use it.
To activate the account select the following link or copy-paste it in your browser:
{ACTIVATE}
After activation you may login to {SITEURL} using the following username and the password you entered during registration:
Username: {USERNAME}