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I cannot see certain exe files in their native folders in Windows Explorer.

I am posting this question because in my five years of professional experience in NT 2000 administration, I have not seen anything like this and I did not find something in Microsoft's support or any other site. I run a 2000 Advanced Server domain controller on a dual xeon Dell machine, and since Monday a very strange problem occurs. When browsing locally with Windows Explorer, I cannot see certain exe files in their native folders (system32 etc) or any other folder. The ones I found so far that I cannot see are services.exe svchost.exe and a kill.exe program I use to kill processes. Even more, I cannot see or find those names in the registry, like something (process or resident program) prevents the system from appearing those names in explorer or regedit (sow hidden files and folders and system files options in folder options are ok) and if I rename a blank txt file to this names the message that it cannot read from source file or folder pops up. Even more, these files do exist and I can browse them from any other pc when opening them from the network (\serverc$wiinnt etc). The server seems to start those services and the only obvious problem with them is that computers belonging to the domain (but in different subnets) are not browseable. The lmhost service does not run properly and the netbios is not routable over tcp/ip (and of course MrxSmb errors in event viewer). The only other change in the computer's behavior is a little window-like message with no words, a yellow exclamation mark and an ok button every time I restart. I don't need to mention that McAfee Enterprise 7 is running fully updated and stinger, pestpatrol, winpatrol, adware, spybot have been used to scan my system with no results. What can cause such a behavior? If it is a virus or something why have no other computers in my network caught it? How do I recover from my problem?
Yikes. I've never heard of these issues before. I'd try an in-place upgrade or repair install then reapply the latest service pack and update with any new hotfixes. If that fails, I assume you have a second domain controller, destroy and re-built the domain controlling having the problems from scratch.

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