I'm using Commerce Kickstart (Drupal 7.23, Kickstart 7.x-2.9). New commerce orders are linked to user accounts. If an account with the same email address does not exist yet, a new account is created. This is the normal flow.
I would like to know in which part of the checkout process, that account is created or linked to, because I've found some cases where the commerce order is linked to anonymous user with no reason.