In wordpress 3.5 users copied from a blog template override original creators admin.
Meaning, if i make a site with admin name: mainadmin
and new blog template has user:
When the template is applied, the website created by userid "mainadmin" is overwritten by the template (instead of appended to the user table)
So then even though the email comes from wordpress engine of a new user site, the user is no longer on the site.
(i copy user tables to allow my support staff to automatically have admin accounts on all subsites.)