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I have gone through my site user list and deleted all duplicate entries. However, when I go to the "Check Permissions" page and search for some users, they still show up twice. One entry has no permissions and one entry is correct. Because of the bad entry, the user can't get into SharePoint and do her job. I can't figure out how to remove that bad user entry.

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Maybe this PowerShell script helps you to find where the rough permission comes from? It gives you a table of user only permission, and permission via group membership.

$urlWeb = "http://sp2010"
Get-SPUser -Web $urlWeb | select UserLogin, @{name=”Exlicit given roles”;expression={$_.Roles}}, @{name=”Roles given via groups”;expression={$_.Groups | %{$_.Roles}}},Groups | format-Table -auto

Reference: How to get user permissions report by using Powershell

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We had the same issue in past, In our case it was Browser issue. After removing the user still showing up. so we did the below steps to fix the issue

  • we clear the browser cache
  • restart the browser

You can try from different PC.

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The People picker is configured via STSADM.exe.

You can set it up with a trust to an authentication provider.

If you have multiple authentication providers (Forms Based Auth, Windows Auth, ADFS etc) and the people picker has been configured for all of them, you may find multiple accounts with the same names...

Please have a look at the following article for people picker setup :

https://technet.microsoft.com/en-us/library/gg602075.aspx

I have seen this issue before... especially with adfs and windows auth since they query the same accounts in AD.

Further reading :

http://curia.me/post/2014/09/11/sharepoint-2013-duplicate-entries-in-people-picker-with-adfs-authentication.aspx

http://www.darrenmarsden.com/post/sharepoint-2013-people-picker-and-duplicate-profiles

i hope I understood your question properly...

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