What is this file about:
C:\WINNT\system32\inetsrv\Metabase.bin

I got the system to scan the harddisk when boot up with the message:
C:\WINNT\system32\inetsrv\Metabase.bin
First allocation unit is not valid.

Well the Metabase.BIN is like a registry file location.  It stores your settings for your IIS Server and other ADSI settings.  You can "look" at it with a tool called Metaedit avaialable at Microsoft.

http://support.microsoft.com/default.aspx?scid=kb;en-us;301386

As for your error message my prognosis is don't fiddle with it if it ain't broke and that error message is NOT indication that it is broke.

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