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I went to central admin via the host name (http://portal.company.com:75000) and went to "Site Actions > Site Permissions" then clicked on "Check Permissions" and a dialog box poped up to enter user/group name. I input user id and resolved it by clicking the man icon. Then clicked on "Check Now" and got an error "File Not Found".

I followed the exact same steps via this url http:/server:75000 and did not get the error.

How do I fix this?

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Can you share the details of your Alternate Access Mapping settings for the central administration web application running on port 75000 –  Arko D Jun 11 '12 at 13:36
    
are you trying on the server itself? If yes, do you experience this behavior using "Run as administrator" on IE ? –  Steve B Jun 11 '12 at 14:12
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Both comments mentioned so far as possibilities. Also I'd suggest looking at LoopBackCheck: http://support.microsoft.com/kb/896861 or switch the authentication method for Central Admin from Kerberos to NTLM if possible (ask your administrators about this, they may not appreciate this).

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