In the last release, a new function made it into the auth plugins confirm_user(). Its called by login/confirm.php if the user clicks on a link in an email to confirm their account.
However, if you confirm an account manually, by visiting admin/user.php and clicking on a confirm link, it simply calls update_record with appropriate values (line 84 at present). This means that any custom hooks that have been built in to confirm_user() in the auth plug-in are lost.
I think admin/user.php should user auth->confirm_user().