Description
On your Windows 2003 server some files in certain folders are missing. However when you rename the folder to other name, the missing files suddenly appear. If you rename the folder back to the original name, the files are missing again. You already check the security permission, possible viruses and malware, but everything seems to be normal.
Resolution
You should check whether you had programs that hide/lock/protect those files from appearing. One of the example is a program called Lock Folder XP. These programs run on Kernel mode and cannot be seen from user mode process monitoring. You can use Rootkit Revealer and Process Explorer from Microsoft SysInternals to try to watch the process.
After you found the program that cause the issue, you can try to uninstall it.
You may need to supply the correct password to uninstall or modify the program.
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