Administrator can't get file ownership or change file permissions

I am not able to modify the file permission in Windows 2000 SP4. I have the admin access. I have around thousand files in the server. I cannot access them nor I can modify it. I am trying to access those files in admin account only, but still getting the same error. When I try to make some changes I am getting error that permission denied. I tried to modify the permissions but that also is not working. How does the privileges of a admin account is limited. How can restore all stuff back again.

Try to run chkdsk. It will scan your system and try to locate any issue. But this is also related to the hard drive error only. There can be some virus or recent updates which has done this. I am sure about the virus. Your server may be infected. Try to check your system by scanning with a good antivirus under safe mode. It is the only way to fix the problem.