I am having a very similar issue to this. Users can login as normal but I cannot run xmlrpc methods. I am also in a multi-site install.
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[4] Authentication successfull for “xxxxx”
…
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[4] Creating user ‘xxxxxx’
…
…
[6] Setting random password.
[2] Sorry, that email address is already used!
[4] – user_id :
[1] Error creating user.
Error creating user!
Has anyone seen this before or found a solution?