Yes should be Native IDE but just checking, as sometimes it is easy to miss some of the easy things when you have a continuing problem such as you are facing.
Have you tried the PC with only the Raptor drive installed. Having the 2nd HDD shouldn't make a difference but sometimes it can so it would be worth eliminating these as a possible cause. I have come across similar issues with both the hard-drives that you are running and the Caviar Black in particular.