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Most probably when run the domain extension script you had the Admin Server up and in fact you did not extended properly the domain.
"You can use the Configuration Wizard only when there is no server running."
Check the script was indeed successful and the domain properly extended by looking in the Admin Server console Servers tab and make sure that what you see there is what you expect. I assume this is not the case.
Thanks for you reply.
I did stop the managed servers as requested by the documentation before extending the domain. Anyway what is not stated in the documentation is that you also have to bounce the admin server after the domain has been extended and before starting the OIM configuration wizard.
Doing so I've been able to solve the issue.