You've convinced me this is a warranty issue. If you forget about the warranty then deep details are needed. For example I ran into this error and had to change the drive AGAIN to a drive that only ran at SATA 1 speed. You may not like that idea or may not bring yourself to do that. I decline to go into the technical reasons why this fixed the issue and similar messages to your machine but since the drive was replaced it is possible they created that same issue.

We also have a bootload of malware out there. Your post revealed too little about how you are sure that's not in play.

Try GRIF'S FINE ADVICE at http://forums.cnet.com/5208-6142_102-0.html?messageID=3105025 for now.
Bob