Hi,
I'm not sure why you are getting duplicate users after the upgrade.
The message you are seeing in the log is logged at "info" level and is informing you of the action the repository it taking to deal with the duplicate user name, it is not an error and from what I can see of the code you should still be able to log in. If you take a look at the users in the UI you should see those that have been duplicated, because when the split occurs one of the users is renamed with GUID attached to the end. Knowing which users have been duplicated may give you some clues as to what is going on.
Cheers,
Roy