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Bootloader virus

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I have been working extensively on this machine, scanned with everything I have, remove hundreds ( upwards or one thousand ) virus's + maleware , worms, everything you can think of, was all downloaded by a tiny exe file in an attachment called ' invoice copy'


This nasty bastage wormed it's way through the entire windows intranet, wreaking havoc each place it set up home. Including momentarily getting the companies domain blacklisted on one certain security network. 


I cannot find this puppy, after roaming through the registry by hand for literally days on end. 


Unless I've just gone through using the windows recovery console to run fixboot and fixmbr, 'something' trashes the bootfile.


I did run the following commands:

	copy c:\windows\system32\config\system c:\windows\tmp\system.bak

	copy c:\windows\system32\config\software c:\windows\tmp\software.bak

	copy c:\windows\system32\config\sam c:\windows\tmp\sam.bak

	copy c:\windows\system32\config\security c:\windows\tmp\security.bak

	copy c:\windows\system32\config\default c:\windows\tmp\default.bak


	delete c:\windows\system32\config\system

	delete c:\windows\system32\config\software

	delete c:\windows\system32\config\sam

	delete c:\windows\system32\config\security

	delete c:\windows\system32\config\default


	copy c:\windows\repair\system c:\windows\system32\config\system

	copy c:\windows\repair\software c:\windows\system32\config\software

	copy c:\windows\repair\sam c:\windows\system32\config\sam

	copy c:\windows\repair\security c:\windows\system32\config\security

	copy c:\windows\repair\default c:\windows\system32\config\default
	Type exit to quit Recovery Console. Your computer will restart.

Hoping the turd was hiding within - no such luck. 


Now I would at this point normally just harvest the documents and needed files, at this point it might be fruitless, since I cannot locate the culprit. 


Yes I have scanned in safe mode, with all the 'popular' tools and removers ect, as well as a few linux based boot disks with the latest updates loaded into memory. 


Suggestions are welcome.

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