Hi Eva,
It has nothing to do with the suggested automatically generate username from customer email option.
Your theme is sending out the wrong template or at least a template with wrong field. Now only a link from the website is send to the new user.
It should look like http://nimb.ws/IC9tE8
This website has the same Woocomerce installation and settings. Please chech because it is a bug!
Kind regads,
Ron