If you are using the standard method of require email activation, then try the following as a test.
In Members.subs.php look for line 782
sendmail($regOptions['email'], $emaildata['subject'], $emaildata['body'], null, null, false, 0);
change that line to
sendmail($regOptions['email'], $emaildata['subject'], $emaildata['body'], null, null, true, 0);
That false to true should force an html copy to go out as well. By default most forum emails don't go out as HTML, I think since they are more likely to be flagged as spam, but TBH I'm not sure.