I remember there was someone with a similar problem, and he could fix it by adding the "domain" path in the configuration. That prevented ownCloud to create 2 different users for the same account.
Yes, I've had this set-up for a while (the domain parameter added in external plugin), and it does not work. I am able to log-in with the domain (user@domain.test) and new user is created - I can see the new user in "Users" page.
The truth is I am running oc 9.1.6.2, not 10.x - might be problem?